Microorganisms and methods for the production of butadiene using acetyl-coA

ABSTRACT

The invention provides non-naturally occurring microbial organisms containing butadiene or 2,4-pentadienoate pathways comprising at least one exogenous nucleic acid encoding a butadiene or 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate. The organism can further contain a hydrogen synthesis pathway. The invention additionally provides methods of using such microbial organisms to produce butadiene or 2,4-pentadienoate by culturing a non-naturally occurring microbial organism containing butadiene or 2,4-pentadienoate pathways as described herein under conditions and for a sufficient period of time to produce butadiene or 2,4-pentadienoate. Hydrogen can be produced together with the production of butadiene or 2,4-pentadienoate.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a divisional of U.S. patent application Ser. No. 15/325,396, filed Jan. 10, 2017, which is a United States National Stage Application under 35 U.S.C. § 371 of International Patent Application No. PCT/US2015/038945, filed Jul. 2, 2015, which claims the benefit of priority of U.S. Provisional Application No. 62/023,786, filed Jul. 11, 2014, the entire contents of each of which are incorporated herein by reference.

BACKGROUND OF THE INVENTION

The present invention relates generally to biosynthetic processes, and more specifically to organisms having 2,4-pentadienoate or butadiene biosynthetic capability.

Over 25 billion pounds of butadiene (1,3-butadiene, BD) are produced annually and is applied in the manufacture of polymers such as synthetic rubbers and ABS resins, and chemicals such as hexamethylenediamine and 1,4-butanediol. Butadiene is typically produced as a by-product of the steam cracking process for conversion of petroleum feedstocks such as naphtha, liquefied petroleum gas, ethane or natural gas to ethylene and other olefins. The ability to manufacture butadiene from alternative and/or renewable feedstocks would represent a major advance in the quest for more sustainable chemical production processes.

One possible way to produce butadiene renewably involves fermentation of sugars or other feedstocks to produce diols, such as 1,4-butanediol or 1,3-butanediol, which are separated, purified, and then dehydrated to butadiene in a second step involving metal-based catalysis. Direct fermentative production of butadiene from renewable feedstocks would obviate the need for dehydration steps and butadiene gas (bp −4.4° C.) would be continuously emitted from the fermenter and readily condensed and collected. Developing a fermentative production process would eliminate the need for fossil-based butadiene and would allow substantial savings in cost, energy, and harmful waste and emissions relative to petrochemically-derived butadiene.

2,4-pentadienoate is a useful substituted butadiene derivative in its own right and a valuable intermediate en route to other substituted 1,3-butadiene derivatives, including, for example, 1-carbamoyl-1,3-butadienes which are accessible via Curtius rearrangement. The resultant N-protected-1,3-butadiene derivatives can be used in Diels alder reactions for the preparation of substituted anilines. 2,4-Pentadienoate can be used in the preparation of various polymers and co-polymers.

Thus, there exists a need for alternative methods for effectively producing commercial quantities of compounds such as 2,4-pentadienoate or butadiene. The present invention satisfies this need and provides related advantages as well.

SUMMARY OF INVENTION

The invention provides non-naturally occurring microbial organisms containing butadiene or 2,4-pentadienoate pathways having at least one exogenous nucleic acid encoding a butadiene or 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate. The invention additionally provides methods of using such microbial organisms to produce butadiene or 2,4-pentadienoate by culturing a non-naturally occurring microbial organism containing butadiene or 2,4-pentadienoate pathways as described herein under conditions and for a sufficient period of time to produce butadiene or 2,4-pentadienoate.

In some embodiments, provided herein is anon-naturally occurring microbial organism containing a butadiene or a 2,4-pentadienoate pathway described herein and further having an acetyl-CoA pathway, a formaldehyde fixation pathway, a methanol metabolic pathway, a formate assimilation pathway, a methanol oxidation pathway, a hydrogenase, a carbon monoxide dehydrogenase, or any combination thereof. In some aspects, the organism includes at least one exogenous nucleic acid encoding at least an enzyme of the acetyl-CoA pathway, the formaldehyde fixation pathway, the methanol metabolic pathway, the formate assimilation pathway, the methanol oxidation pathway, the hydrogenase, or any combination thereof, that is expressed in a sufficient amount to enhance the availability of acetyl-CoA or reducing equivalents. Such organisms of the invention advantageously enhance the production of substrates and/or pathway intermediates for the production of butadiene, 2,4-pentadienoate or hydrogen.

In some embodiments, provided herein is a non-naturally occurring microbial organism containing a butadiene or a 2,4-pentadienoate pathway described herein and further includes attenuation of one or more endogenous enzymes, which enhances carbon flux through acetyl-CoA, or a gene disruption of one or more endogenous nucleic acids encoding such enzymes. For example, in some aspects, the endogenous enzyme can be selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof.

In some embodiments, provided herein is a non-naturally occurring microbial organism containing a butadiene or a 2,4-pentadienoate pathway described herein and further having a hydrogen synthesis pathway catalyzing the synthesis of hydrogen from a reducing equivalent, wherein the hydrogen synthesis pathway includes an enzyme selected from the group consisting of a hydrogenase, a formate-hydrogene lyase and ferredoxin: NADP+ oxidoreductase. In one aspect, the reducing equivalent is selected from the group consisting of NADH, NADPH, FADH, reduced quinones, reduced ferredoxins, reduced flavodoxins or reduced thioredoxins

In some embodiments, provided herein is a method for producing a combination of butadiene and hydrogen or of 2,4-pentadienoate and hydrogen including culturing anon-naturally occurring microbial organism disclosed herein under conditions and for a sufficient period of time to produce a butadiene and hydrogen or 2,4-pentadienoate and hydrogen.

In some embodiments, provided herein is bioderived butadiene, 2,4-pentadienoate or hydrogen produced according to a method disclosed herein. In some embodiments, provided herein is a biobased product having the bioderived butadiene, 2,4-pentadienoate or hydrogen.

In some embodiments, provided herein is a process for producing hydrogen including (a) culturing anon-naturally culturing microbial organism disclosed herein in a substantially anaerobic culture medium under a condition to produce hydrogen; (b) separating the produced hydrogen from the culture medium; and (c) collecting the separated hydrogen.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows exemplary pathways to form butadiene and 2,4-pentadienoate via 2-oxopentenoate. The enzymes are: A. Acetaldehyde dehydrogenase, B. 4-hydroxy 2-oxovalerate aldolase, C. 4-hydroxy 2-oxovalerate dehydratase, D. 2-oxopentenoate reductase, E. 2-hydroxypentenoate dehydratase, F. 2,4-pentadienoate decarboxylase, G. 2-oxopentenoate ligase, H. 2-oxopentenoate:acetyl CoA CoA transferase, I. 2-oxopentenoyl-CoA reductase, J. 2-hydroxypentenoate ligase, K. 2-hydroxypentenoate:acetyl-CoA CoA transferase, L. 2-hydroxypentenoyl-CoA dehydratase, M. 2,4-Pentadienoyl-CoA hydrolase, N. 2,4-Pentadienoyl-CoA:acetyl CoA CoA transferase.

FIG. 2 shows exemplary pathways to form butadiene and 2,4-pentadienoate via 3-oxoglutaryl-CoA. The enzymes are: A. Acetyl-CoA carboxylase, B. malonyl-CoA:acetyl-CoA acyltransferase, C. 3-Oxoglutaryl-CoA reductase (ketone-reducing), D. 3-hydroxyglutaryl-CoA reductase (aldehyde forming), E. 3-hydroxy-5-oxopentanoate reductase, F. 3-hydroxyglutaryl-CoA reductase (alcohol forming), G. 3,5-dihydroxypentanoate dehydratase, H. 5-hydroxypent-2-enoate dehydratase, I. 2,4-pentadienoate decarboxylase, G. 3,5-dihydroxypentanoate ligase, K. 3,5-dihydroxypentanoate:acetyl-CoA CoA transferase, L. 3,5-dihydroxypentanoyl-CoA dehydratase, M. 5-hydroxypent-2-enoate ligase, N. 5-hydroxypent-2-enoate:acetyl-CoA CoA transferase, O. 5-hydroxypent-2-enoyl-CoA hydrolase, P. 2,4-pentadienoyl-CoA CoA hydrolase, Q. 2,4-pentadienoyl-CoA:acetyl-CoA CoA transferase, R. Phosphate-3-hydroxyglutaryl transferase, S. 3-hydroxy-5-oxopentanoate synthase.

FIG. 3 shows exemplary metabolic pathways enabling the conversion of CO2, formate, formaldehyde (Fald), methanol (MeOH), glycerol, xylose (XYL) and glucose (GLC) to acetyl-CoA (ACCOA) and exemplary endogenous enzyme targets for optional attenuation or disruption. The exemplary pathways can be combined with bioderived compound pathways, including the pathways depicted herein that utilize ACCOA, such as those depicted in FIGS. 1-2. The enzyme targets are indicated by arrows having “X” markings. The endogenous enzyme targets include DHA kinase, methanol oxidase (AOX), PQQ-dependent methanol dehydrogenase (PQQ) and/or DHA synthase. The enzymes are: A. methanol dehydrogenase, B. 3-hexulose-6-phosphate synthase, C. 6-phospho-3-hexuloisomerase, D. dihydroxyacetone synthase, E. formate reductase, F. formate ligase, formate transferase, or formate synthetase, G. formyl-CoA reductase, H. formyltetrahydrofolate synthetase, I. methenyltetrahydrofolate cyclohydrolase, J. methylenetetrahydrofolate dehydrogenase, K. spontaneous or formaldehyde-forming enzyme, L. glycine cleavage system, M. serine hydroxymethyltransferase, N. serine deaminase, O. methylenetetrahydrofolate reductase, P. acetyl-CoA synthase, Q. pyruvate formate lyase, R pyruvate dehydrogenase, pyruvate ferredoxin oxidoreductase, or pyruvate:NADP+ oxidoreductase, S. formate dehydrogenase, T. fuctose-6-phosphate phosphoketolase, U. xylulose-5-phosphate phosphoketolase, V. phosphotransacetylase, W. acetate kinase, X. acetyl-CoA transferase, synthetase, or ligase, Y. lower glycolysis including glyceraldehyde-3-phosphate dehydrogenase, Z. fuctose-6-phosphate aldolase.

FIG. 4 shows exemplary metabolic pathways that provide the extraction of reducing equivalents from methanol, hydrogen, or carbon monoxide. The enzymes are: A. methanol methyltransferase, B. methylenetetrahydrofolate reductase, C. methylenetetrahydrofolate dehydrogenase, D. methenyltetrahydrofolate cyclohydrolase, E. formyltetrahydrofolate deformylase, F. formyltetrahydrofolate synthetase, G. formate hydrogen lyase, H. hydrogenase, I. formate dehydrogenase, J. methanol dehydrogenase, K. spontaneous or formaldehyde activating enzyme, L. formaldehyde dehydrogenase, M. spontaneous or S-(hydroxymethyl)glutathione synthase, N. Glutathione-Dependent Formaldehyde Dehydrogenase, O. S-formylglutathione hydrolase, P. carbon monoxide dehydrogenase. See abbreviation list below for compound names.

FIG. 5 shows the carbon flux distribution of a butadiene pathway via 4-hydroxy 2-oxovalerate when incorporating the phoshoketolase pathway. The theoretical yield of the pathway is improved from 1 mol butadiene per mole glucose to 1.09 mole butadiene per mole glucose. See abbreviation list below for compound names.

DETAILED DESCRIPTION OF THE INVENTION

Provided herein is the design and production of cells and organisms having biosynthetic production capabilities for butadiene or 2,4-pentadienoate. The invention, in particular, relates to the design of microbial organisms capable of producing butadiene or 2,4-pentadienoate by introducing one or more nucleic acids encoding a butadiene or 2,4-pentadienoate pathway enzyme.

The following is a list of abbreviations and their corresponding compound or composition names. These abbreviations, which are used throughout the disclosure and the figures. It is understood that one of ordinary skill in the art can readily identify these compounds/compositions by such nomenclature: MeOH or MEOH=methanol; Fald=formaldehyde; GLC=glucose; G6P=glucose-6-phosphate; H6P=hexulose-6-phosphate; F6P=fuctose-6-phosphate; FDP=fuctose diphosphate or fuctose-1,6-diphosphate; DHA=dihydroxyacetone; DHAP=dihydroxyacetone phosphate; G3P=glyceraldehyde-3-phosphate; PYR=pyruvate; ACTP=acetyl-phosphate; ACCOA=acetyl-CoA; AACOA=acetoacetyl-CoA; MALCOA=malonyl-CoA; FIHF=formyltetrahydrofolate; THF=tetrahydrofolate; E4P=erythrose-4-phosphate: Xu5P=xyulose-5-phosphate; Ru5P=ribulose-5-phosphate; S7P=sedoheptulose-7-phosphate: R5P=ribose-5-phosphate; XYL=xylose; TCA=tricarboxylic acid; PEP=Phosphoenolpyruvate; OAA=Oxaloacetate; MAL=malate.

Pathways identified herein, and particularly pathways exemplified in specific combinations presented herein, are superior over other pathways based in part on the applicant's ranking of pathways based on attributes including maximum theoretical yield, maximal carbon flux, maximal production of reducing equivalents, minimal production of CO2, pathway length, number of non-native steps, thermodynamic feasibility, number of enzymes active on pathway substrates or structurally similar substrates, and having steps with currently characterized enzymes, and furthermore, the latter pathways are even more favored by having in addition at least the fewest number of non-native steps required, the most enzymes known active on pathway substrates or structurally similar substrates, and the fewest total number of steps from central metabolism.

In one embodiment, the invention utilizes in silico stoichiometric models of Escherichia coli metabolism that identify metabolic designs for biosynthetic production of butadiene or 2,4-pentadienoate. The results described herein indicate that metabolic pathways can be designed and recombinantly engineered to achieve the biosynthesis of butadiene or 2,4-pentadienoate in Escherichia coli and other cells or organisms. Biosynthetic production of butadiene or 2,4-pentadienoate, for example, for the in silico designs can be confirmed by construction of strains having the designed metabolic genotype. These metabolically engineered cells or organisms also can be subjected to adaptive evolution to further augment butadiene or 2,4-pentadienoate biosynthesis, including under conditions approaching theoretical maximum growth.

In certain embodiments, the butadiene or 2,4-pentadienoate biosynthesis characteristics of the designed strains make them genetically stable and particularly useful in continuous bioprocesses. Separate strain design strategies were identified with incorporation of different non-native or heterologous reaction capabilities into E. coli or other host organisms leading to butadiene or 2,4-pentadienoate producing metabolic pathways from acetyl-CoA. In silico metabolic designs were identified that resulted in the biosynthesis of butadiene or 2,4-pentadienoate in microorganisms from each of these substrates or metabolic intermediates.

Strains identified via the computational component of the platform can be put into actual production by genetically engineering any of the predicted metabolic alterations, which lead to the biosynthetic production of butadiene or 2,4-pentadienoate or other intermediate and/or downstream products. In yet a further embodiment, strains exhibiting biosynthetic production of these compounds can be further subjected to adaptive evolution to further augment product biosynthesis. The levels of product biosynthesis yield following adaptive evolution also can be predicted by the computational component of the system.

As used herein, the term “non-naturally occurring” when used in reference to a microbial organism or microorganism of the invention is intended to mean that the microbial organism has at least one genetic alteration not normally found in a naturally occurring strain of the referenced species, including wild-type strains of the referenced species. Genetic alterations include, for example, modifications introducing expressible nucleic acids encoding metabolic polypeptides, other nucleic acid additions, nucleic acid deletions and/or other functional disruption of the microbial organism's genetic material. Such modifications include, for example, coding regions and functional fragments thereof, for heterologous, homologous or both heterologous and homologous polypeptides for the referenced species. Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a gene or operon. Exemplary metabolic polypeptides include enzymes or proteins within a butadiene or 2,4-pentadienoate biosynthetic pathway.

A metabolic modification refers to a biochemical reaction that is altered from its naturally occurring state. Therefore, non-naturally occurring microorganisms can have genetic modifications to nucleic acids encoding metabolic polypeptides, or functional fragments thereof. Exemplary metabolic modifications are disclosed herein.

As used herein, the term “isolated” when used in reference to a microbial organism is intended to mean an organism that is substantially free of at least one component as the referenced microbial organism is found in nature. The term includes a microbial organism that is removed from some or all components as it is found in its natural environment. The term also includes a microbial organism that is removed from some or all components as the microbial organism is found in non-naturally occurring environments. Therefore, an isolated microbial organism is partly or completely separated from other substances as it is found in nature or as it is grown, stored or subsisted in non-naturally occurring environments. Specific examples of isolated microbial organisms include partially pure microbes, substantially pure microbes and microbes cultured in a medium that is non-naturally occurring.

As used herein, the terms “microbial,” “microbial organism” or “microorganism” are intended to mean any organism that exists as a microscopic cell that is included within the domains of archaea, bacteria or eukarya. Therefore, the term is intended to encompass prokaryotic or eukaryotic cells or organisms having a microscopic size and includes bacteria, archaea and eubacteria of all species as well as eukaryotic microorganisms such as yeast and fungi. The term also includes cell cultures of any species that can be cultured for the production of a biochemical.

As used herein, the term “CoA” or “coenzyme A” is intended to mean an organic cofactor or prosthetic group (nonprotein portion of an enzyme) whose presence is required for the activity of many enzymes (the apoenzyme) to form an active enzyme system. Coenzyme A functions in certain condensing enzymes, acts in acetyl or other acyl group transfer and in fatty acid synthesis and oxidation, pyruvate oxidation and in other acetylation.

As used herein, the term “substantially anaerobic” when used in reference to a culture or growth condition is intended to mean that the amount of oxygen is less than about 10% of saturation for dissolved oxygen in liquid media. The term also is intended to include sealed chambers of liquid or solid medium maintained with an atmosphere of less than about 1% oxygen.

“Exogenous” as it is used herein is intended to mean that the referenced molecule or the referenced activity is introduced into the host microbial organism. The molecule can be introduced, for example, by introduction of an encoding nucleic acid into the host genetic material such as by integration into a host chromosome or as non-chromosomal genetic material such as a plasmid. Therefore, the term as it is used in reference to expression of an encoding nucleic acid refers to introduction of the encoding nucleic acid in an expressible form into the microbial organism. When used in reference to a biosynthetic activity, the term refers to an activity that is introduced into the host reference organism. The source can be, for example, a homologous or heterologous encoding nucleic acid that expresses the referenced activity following introduction into the host microbial organism. Therefore, the term “endogenous” refers to a referenced molecule or activity that is present in the host. Similarly, the term when used in reference to expression of an encoding nucleic acid refers to expression of an encoding nucleic acid contained within the microbial organism. The term “heterologous” refers to a molecule or activity derived from a source other than the referenced species whereas “homologous” refers to a molecule or activity derived from the host microbial organism. Accordingly, exogenous expression of an encoding nucleic acid of the invention can utilize either or both a heterologous or homologous encoding nucleic acid.

It is understood that when more than one exogenous nucleic acid is included in a microbial organism that the more than one exogenous nucleic acids refers to the referenced encoding nucleic acid or biosynthetic activity, as discussed above. It is further understood, as disclosed herein, that such more than one exogenous nucleic acids can be introduced into the host microbial organism on separate nucleic acid molecules, on polycistronic nucleic acid molecules, or a combination thereof, and still be considered as more than one exogenous nucleic acid. For example, as disclosed herein a microbial organism can be engineered to express two or more exogenous nucleic acids encoding a desired pathway enzyme or protein. In the case where two exogenous nucleic acids encoding a desired activity are introduced into a host microbial organism, it is understood that the two exogenous nucleic acids can be introduced as a single nucleic acid, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two exogenous nucleic acids. Similarly, it is understood that more than two exogenous nucleic acids can be introduced into a host organism in any desired combination, for example, on a single plasmid, on separate plasmids, can be integrated into the host chromosome at a single site or multiple sites, and still be considered as two or more exogenous nucleic acids, for example three exogenous nucleic acids. Thus, the number of referenced exogenous nucleic acids or biosynthetic activities refers to the number of encoding nucleic acids or the number of biosynthetic activities, not the number of separate nucleic acids introduced into the host organism.

As used herein, the term “gene disruption,” or grammatical equivalents thereof, is intended to mean a genetic alteration that renders the encoded gene product inactive or attenuated. The genetic alteration can be, for example, deletion of the entire gene, deletion of a regulatory sequence required for transcription or translation, deletion of a portion of the gene which results in a truncated gene product, or by any of various mutation strategies that inactivate or attenuate the encoded gene product. One particularly useful method of gene disruption is complete gene deletion because it reduces or eliminates the occurrence of genetic reversions in the non-naturally occurring microorganisms of the invention. A gene disruption also includes a null mutation, which refers to a mutation within a gene or a region containing a gene that results in the gene not being transcribed into RNA and/or translated into a functional gene product. Such a null mutation can arise from many types of mutations including, for example, inactivating point mutations, deletion of a portion of a gene, entire gene deletions, or deletion of chromosomal segments.

As used herein, the term “growth-coupled” when used in reference to the production of a biochemical product is intended to mean that the biosynthesis of the referenced biochemical product is produced during the growth phase of a microorganism. In a particular embodiment, the growth-coupled production can be obligatory, meaning that the biosynthesis of the referenced biochemical is an obligatory product produced during the growth phase of a microorganism.

As used herein, the term “attenuate,” or grammatical equivalents thereof, is intended to mean to weaken, reduce or diminish the activity or amount of an enzyme or protein. Attenuation of the activity or amount of an enzyme or protein can mimic complete disruption if the attenuation causes the activity or amount to fall below a critical level required for a given pathway to function. However, the attenuation of the activity or amount of an enzyme or protein that mimics complete disruption for one pathway, can still be sufficient for a separate pathway to continue to function. For example, attenuation of an endogenous enzyme or protein can be sufficient to mimic the complete disruption of the same enzyme or protein for production of a butadiene or 2,4-pentadienoate of the invention, but the remaining activity or amount of enzyme or protein can still be sufficient to maintain other pathways, such as a pathway that is critical for the host microbial organism to survive, reproduce or grow. Attenuation of an enzyme or protein can also be weakening, reducing or diminishing the activity or amount of the enzyme or protein in an amount that is sufficient to increase yield of butadiene or 2,4-pentadienoate of the invention, but does not necessarily mimic complete disruption of the enzyme or protein.

The non-naturally occurring microbal organisms of the invention can contain stable genetic alterations, which refers to microorganisms that can be cultured for greater than five generations without loss of the alteration. Generally, stable genetic alterations include modifications that persist greater than 10 generations, particularly stable modifications will persist more than about 25 generations, and more particularly, stable genetic modifications will be greater than 50 generations, including indefinitely.

In the case of gene disruptions, a particularly useful stable genetic alteration is a gene deletion. The use of a gene deletion to introduce a stable genetic alteration is particularly useful to reduce the likelihood of a reversion to a phenotype prior to the genetic alteration. For example, stable growth-coupled production of a biochemical can be achieved, for example, by deletion of a gene encoding an enzyme catalyzing one or more reactions within a set of metabolic modifications. The stability of growth-coupled production of a biochemical can be further enhanced through multiple deletions, significantly reducing the likelihood of multiple compensatory reversions occurring for each disrupted activity.

Those skilled in the art will understand that the genetic alterations, including metabolic modifications exemplified herein, are described with reference to a suitable host organism such as E. coli and their corresponding metabolic reactions or a suitable source organism for desired genetic material such as genes for a desired metabolic pathway. However, given the complete genome sequencing of a wide variety of organisms and the high level of skill in the area of genomics, those skilled in the art will readily be able to apply the teachings and guidance provided herein to essentially all other organisms. For example, the E. coli metabolic alterations exemplified herein can readily be applied to other species by incorporating the same or analogous encoding nucleic acid from species other than the referenced species. Such genetic alterations include, for example, genetic alterations of species homologs, in general, and in particular, orthologs, paralogs or nonorthologous gene displacements.

An ortholog is a gene or genes that are related by vertical descent and are responsible for substantially the same or identical functions in different organisms. For example, mouse epoxide hydrolase and human epoxide hydrolase can be considered orthologs for the biological function of hydrolysis of epoxides. Genes are related by vertical descent when, for example, they share sequence similarity of sufficient amount to indicate they are homologous, or related by evolution from a common ancestor. Genes can also be considered orthologs if they share three-dimensional structure but not necessarily sequence similarity, of a sufficient amount to indicate that they have evolved from a common ancestor to the extent that the primary sequence similarity is not identifiable. Genes that are orthologous can encode proteins with sequence similarity of about 25% to 100% amino acid sequence identity. Genes encoding proteins sharing an amino acid similarity less that 25% can also be considered to have arisen by vertical descent if their three-dimensional structure also shows similarities. Members of the serine protease family of enzymes, including tissue plasminogen activator and elastase, are considered to have arisen by vertical descent from a common ancestor.

Orthologs include genes or their encoded gene products that through, for example, evolution, have diverged in structure or overall activity. For example, where one species encodes a gene product exhibiting two functions and where such functions have been separated into distinct genes in a second species, the three genes and their corresponding products are considered to be orthologs. For the production of a biochemical product, those skilled in the art will understand that the orthologous gene harboring the metabolic activity to be introduced or disrupted is to be chosen for construction of the non-naturally occurring microorganism. An example of orthologs exhibiting separable activities is where distinct activities have been separated into distinct gene products between two or more species or within a single species. A specific example is the separation of elastase proteolysis and plasminogen proteolysis, two types of serine protease activity, into distinct molecules as plasminogen activator and elastase. A second example is the separation of mycoplasma 5′-3′ exonuclease and Drosophila DNA polymerase III activity. The DNA polymerase from the first species can be considered an ortholog to either or both of the exonuclease or the polymerase from the second species and vice versa.

In contrast, paralogs are homologs related by, for example, duplication followed by evolutionary divergence and have similar or common, but not identical functions. Paralogs can originate or derive from, for example, the same species or from a different species. For example, microsomal epoxide hydrolase (epoxide hydrolase I) and soluble epoxide hydrolase (epoxide hydrolase II) can be considered paralogs because they represent two distinct enzymes, co-evolved from a common ancestor, that catalyze distinct reactions and have distinct functions in the same species. Paralogs are proteins from the same species with significant sequence similarity to each other suggesting that they are homologous, or related through co-evolution from a common ancestor. Groups of paralogous protein families include HipA homologs, luciferase genes, peptidases, and others.

A nonorthologous gene displacement is a nonorthologous gene from one species that can substitute for a referenced gene function in a different species. Substitution includes, for example, being able to perform substantially the same or a similar function in the species of origin compared to the referenced function in the different species. Although generally, a nonorthologous gene displacement will be identifiable as structurally related to a known gene encoding the referenced function, less structurally related but functionally similar genes and their corresponding gene products nevertheless will still fall within the meaning of the term as it is used herein. Functional similarity requires, for example, at least some structural similarity in the active site or binding region of a nonorthologous gene product compared to a gene encoding the function sought to be substituted. Therefore, a nonorthologous gene includes, for example, a paralog or an unrelated gene.

Therefore, in identifying and constructing the non-naturally occurring microbial organisms of the invention having butadiene or 2,4-pentadienoate biosynthetic capability, those skilled in the art will understand with applying the teaching and guidance provided herein to a particular species that the identification of metabolic modifications can include identification and inclusion or inactivation of orthologs. To the extent that paralogs and/or nonorthologous gene displacements are present in the referenced microorganism that encode an enzyme catalyzing a similar or substantially similar metabolic reaction, those skilled in the art also can utilize these evolutionally related genes. Similarly for a gene disruption, evolutionally related genes can also be disrupted or deleted in a host microbial organism to reduce or eliminate functional redundancy of enzymatic activities targeted for disruption.

Orthologs, paralogs and nonorthologous gene displacements can be determined by methods well known to those skilled in the art. For example, inspection of nucleic acid or amino acid sequences for two polypeptides will reveal sequence identity and similarities between the compared sequences. Based on such similarities, one skilled in the art can determine if the similarity is sufficiently high to indicate the proteins are related through evolution from a common ancestor. Algorithms well known to those skilled in the art, such as Align, BLAST, Clustal W and others compare and determine a raw sequence similarity or identity, and also determine the presence or significance of gaps in the sequence which can be assigned a weight or score. Such algorithms also are known in the art and are similarly applicable for determining nucleotide sequence similarity or identity. Parameters for sufficient similarity to determine relatedness are computed based on well known methods for calculating statistical similarity, or the chance of finding a similar match in a random polypeptide, and the significance of the match determined. A computer comparison of two or more sequences can, if desired, also be optimized visually by those skilled in the art. Related gene products or proteins can be expected to have a high similarity, for example, 25% to 100% sequence identity. Proteins that are unrelated can have an identity which is essentially the same as would be expected to occur by chance, if a database of sufficient size is scanned (about 5%). Sequences between 5% and 24% mayor may not represent sufficient homology to conclude that the compared sequences are related. Additional statistical analysis to determine the significance of such matches given the size of the data set can be carried out to determine the relevance of these sequences.

Exemplary parameters for determining relatedness of two or more sequences using the BLAST algorithm, for example, can be as set forth below. Briefly, amino acid sequence alignments can be performed using BLASTP version 2.0.8 (Jan. 5, 1999) and the following parameters: Matrix: 0 BLOSUM62; gap open: 11; gap extension: 1; x_dropoff 50; expect: 10.0; wordsize: 3; filter: on. Nucleic acid sequence alignments can be performed using BLASTN version 2.0.6 (Sep. 16, 1998) and the following parameters: Match: 1; mismatch: −2; gap open: 5; gap extension: 2; x_dropoff: 50; expect: 10.0; wordsize: 11; filter: off. Those skilled in the art will know what modifications can be made to the above parameters to either increase or decrease the stringency of the comparison, for example, and determine the relatedness of two or more sequences.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway, having at least one exogenous nucleic acid encoding a butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, wherein the butadiene pathway includes a pathway shown in FIGS. 1 and 2 selected from: (1) 1A, 1B, 1C, 1G, 1I, 1L, 1M, and 1F; (2) 1A, 1B, 1C, 1G, 1I, 1L, 1N, and 1F; (3) 1A, 1B, 1C, 1H, 1I, 1L, 1M, and 1F; (4) 1A, 1B, 1C, 1H, 1I, 1L, 1N, and 1F; (5) 1A, 1B, 1C, 1D, 1J, 1L, 1M, and 1F; (6) 1A, 1B, 1C, 1D, 1J, 1L, 1N, and 1F; (7) 1A, 1B, 1C, 1D, 1K, 1L, 1M, and 1F; (8) 1A, 1B, 1C, 1D, 1K, 1L, 1N, and 1F; (9) 1B, 1C, 1G, 1, 1L, 1M, and 1F; (10) 1B, 1C, 1G, 1I, 1L, 1N, and 1F; (11) 1B, 1C, 1H, 1I, 1L, 1M, and 1F; (12) 1B, 1C, 1H, 1I, 1L, 1N, and 1F; (13) 1B, 1C, 1D, 1J, 1L, 1M, and 1F; (14) 1B, 1C, 1D, 1J, 1L, 1N, and 1F; (15) 1B, 1C, 1D, 1K, 1L, 1M, and 1F; (16) 1B, 1C, 1D, 1K, 1L, 1N, and 1F; (17) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2Q, and 2I; (18) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2P, and 2I; (19) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2Q, and 2I; (20) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2P, and 2I; (21) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2Q, and 2I; (22) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2P, and 2I; (23) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2Q, and 2I; (24) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2P, and 2I; (25) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2H, and 2I; (26) 2A, 2B, 2C, 2D, 2E, 2J, 2L, 2O, 2Q, and 2I; (27) 2A, 2B, 2C, 2D, 2E; 2J, 2L, 2O, 2P, and 2I; (28) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2Q, and 2I; (29) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2P, and 2I; (30) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2Q, and 2I; (31) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2P, and 2I; (32) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2Q, and 2I; (33) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2P, and 2I; (34) 2A, 2B, 2C, 2F, 2J, 2L, 2O, 2Q, and 2I; (35) 2A, 2B, 2C, 2F, 2J, 2L, 2O, 2P, and 2I; (36) 2A, 2B, 2C, 2F, 2K, 2L, 2O, 2Q, and 2I; (37) 2A, 2B, 2C, 2F, 2K, 2L, 2O, 2P, and 2I; (38) 2A, 2B, 2C, 2F, 2G, 2M, 2O, 2Q, and 2I; (39) 2A, 2B, 2C, 2F, 2G, 2M, 2O, 2P, and 2I; (40) 2A, 2B, 2C, 2F, 2G, 2N, 2O, 2Q, and 2I; (41) 2A, 2B, 2C, 2F, 2G, 2N, 2O, 2P, and 2I; (42) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2Q, and 2I; (43) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2P, and 2I; (44) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2Q, and 2I; (45) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2P, and 2I; (46) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2Q, and 2I; (47) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2P, and 2I; (48) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2Q, and 2I; (49) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2P, and 2I; (50) 2B, 2C, 2R, 2S, 2E, 2G, 2H, and 2I; (51) 2B, 2C, 2D, 2E, 2J, 2L, 2O, 2Q, and 2I; (52) 2B, 2C, 2D, 2E, 2J, 2L, 2O, 2P, and 2I; (53) 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2Q, and 2I; (54) 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2P, and 2I; (55) 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2Q, and 2I; (56) 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2P, and 2I; (57) 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2Q, and 2I; (58) 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2P, and 2I; (59) 2B, 2C, 2F, 2J, 2L, 2O, 2Q, and 2I; (60) 2B, 2C, 2F, 2J, 2L, 2O, 2P, and 2I; (61) 2B, 2C, 2F, 2K, 2L, 2O, 2Q, and 2I; (62) 2B, 2C, 2F, 2K, 2L, 2O, 2P, and 2I; (63) 2B, 2C, 2F, 2G, 2M, 2O, 2Q, and 2I; (64) 2B, 2C, 2F, 2G, 2M, 2O, 2P, and 2I; (65) 2B, 2C, 2F, 2G, 2N, 2O, 2Q, and 2I; (66) 2B, 2C, 2F, 2G, 2N, 2O, 2P, and 2I; (67) 1C, 1G, 1I, 1L, 1M, and 1F; (68) 1C, 1G, 1I, 1L, 1N, and 1F; (69) 1C, 1H, 1I, 1L, 1M, and 1F; (70) 1C, 1H, 1I, 1L, 1N, and 1F; (71) 1C, 1D, 1J, 1L, 1M, and 1F; (72) 1C, 1D, 1J, 1L, 1N, and 1F; (73) 1C, 1D, 1K, 1L, 1M, and 1F; (74) 1C, 1D, 1K, 1L, 1N, and 1F; (75) 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2Q, and 2I; (76) 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2P, and 2I; (77) 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2Q, and 2I; (78) 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2P, and 2I; (79) 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2Q, and 2I; (80) 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2P, and 2I; (81) 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2Q, and 2I; (82) 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2P, and 2I; (83) 2C, 2R, 2S, 2E, 2G, 2H, and 2I; (84) 2C, 2D, 2E, 2J, 2L, 2O, 2Q, and 2I; (85) 2C, 2D, 2E, 2J, 2L, 2O, 2P, and 2I; (86) 2C, 2D, 2E, 2K, 2L, 2O, 2Q, and 2I; (87) 2C, 2D, 2E, 2K, 2L, 2O, 2P, and 2I; (88) 2C, 2D, 2E, 2G, 2M, 2O, 2Q, and 2I; (89) 2C, 2D, 2E, 2G, 2M, 2O, 2P, and 2I; (90) 2C, 2D, 2E, 2G, 2N, 2O, 2Q, and 2I; (91) 2C, 2D, 2E, 2G, 2N, 2O, 2P, and 2I; (92) 2C, 2F, 2J, 2L, 2O, 2Q, and 2I; (93) 2C, 2F, 2J, 2L, 2O, 2P, and 2I; (94) 2C, 2F, 2K, 2L, 2O, 2Q, and 2I; (95) 2C, 2F, 2K, 2L, 2O, 2P, and 2I; (96) 2C, 2F, 2G, 2M, 2O, 2Q, and 2I; (97) 2C, 2F, 2G, 2M, 2O, 2P, and 2I; (98) 2C, 2F, 2G, 2N, 2O, 2Q, and 2I; and (99) 2C, 2F, 2G, 2N, 2O, 2P, and 2I, wherein 1A is an acetaldehyde dehydrogenase, wherein 1B is a 4-hydroxy 2-oxovalerate aldolase, wherein 1C is a 4-hydroxy 2-oxovalerate dehydratase, wherein 1D is a 2-oxopentenoate reductase, wherein 1E is a 2-hydroxypentenoate dehydratase, wherein 1F is a 2,4-pentadienoate decarboxylase, wherein 1G is a 2-oxopentenoate ligase, wherein 1H is a 2-oxopentenoate:acetyl CoA CoA transferase, wherein 1I is a 2-oxopentenoyl-CoA reductase, wherein 1J is a 2-hydroxypentenoate ligase, wherein 1K is a 2-hydroxypentenoate:acetyl-CoA CoA transferase, wherein 1L is a 2-hydroxypentenoyl-CoA dehydratase, wherein 1M is a 2,4-Pentadienoyl-CoA hydrolase, wherein 1N is a 2,4-Pentadienoyl-CoA:acetyl CoA CoA transferase, wherein 2A is an acetyl-CoA carboxylase, wherein 2B is a malonyl-CoA:acetyl-CoA acyltransferase, wherein 2C is a 3-Oxoglutaryl-CoA reductase (ketone-reducing), wherein 2D is a 3-hydroxyglutaryl-CoA reductase (aldehyde forming), wherein 2E is a 3-hydroxy-5-oxopentanoate reductase, wherein 2F is a 3-hydroxyglutaryl-CoA reductase (alcohol forming), wherein 2G is a 3,5-dihydroxypentanoate dehydratase, wherein 2H is a 5-hydroxypent-2-enoate dehydratase, wherein 2I is a 2,4-pentadienoate decarboxylase, wherein 2I is a 3,5-dihydroxypentanoate ligase, wherein 2K is a 3,5-dihydroxypentanoate:acetyl-CoA CoA transferase, wherein 2L is a 3,5-dihydroxypentanoyl-CoA dehydratase, wherein 2M is a 5-hydroxypent-2-enoate ligase, wherein 2N is a 5-hydroxypent-2-enoate:acetyl-CoA CoA transferase, wherein 2O is a 5-hydroxypent-2-enoyl-CoA hydrolase, wherein 2P is a 2,4-pentadienoyl-CoA CoA hydrolase, wherein 2Q is a 2,4-pentadienoyl-CoA:acetyl-CoA CoA transferase, wherein 2R is a Phosphate-3-hydroxyglutaryl transferase, and wherein 2S is a 3-hydroxy-5-oxopentanoate synthase.

In some embodiments, the butadiene pathway includes (1) 1A, 1B, 1C, 1G, 1I, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (2) 1A, 1B, 1C, 1G, 1I, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (3) 1A, 1B, 1C, 1H, 1I, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (4) 1A, 1B, 1C, 1H, 1, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (5) 1A, 1B, 1C, 1D, 1J, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (6) 1A, 1B, 1C, 1D, 1J, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (7) 1A, 1B, 1C, 1D, 1K, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (8) 1A, 1B, 1C, 1D, 1K, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (9) 1B, 1C, 1G, 1I, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (10) 1B, 1C, 1G, 1I, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (11) 1B, 1C, 1H, 1I, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (12) 1B, 1C, 1H, 1I, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (13) 1B, 1C, 1D, 1J, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (14) 1B, 1C, 1D, 1J, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (15) 1B, 1C, 1D, 1K, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (16) 1B, 1C, 1D, 1K, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (17) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (18) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (19) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (20) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (21) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (22) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (23) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (24) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (25) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2H, and 2I. In some embodiments, the butadiene pathway includes (26) 2A, 2B, 2C, 2D, 2E, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (27) 2A, 2B, 2C, 2D, 2E; 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (28) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (29) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (30) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (31) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (32) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (33) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (34) 2A, 2B, 2C, 2F, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (35) 2A, 2B, 2C, 2F, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (36) 2A, 2B, 2C, 2F, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (37) 2A, 2B, 2C, 2F, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (38) 2A, 2B, 2C, 2F, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (39) 2A, 2B, 2C, 2F, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (40) 2A, 2B, 2C, 2F, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (41) 2A, 2B, 2C, 2F, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (42) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (43) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (44) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (45) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (46) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (47) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (48) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (49) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (50) 2B, 2C, 2R, 2S, 2E, 2G, 2H, and 2I. In some embodiments, the butadiene pathway includes (51) 2B, 2C, 2D, 2E, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (52) 2B, 2C, 2D, 2E, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (53) 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (54) 2B, 2C, 2D, 2E, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (55) 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (56) 2B, 2C, 2D, 2E, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (57) 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (58) 2B, 2C, 2D, 2E, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (59) 2B, 2C, 2F, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (60) 2B, 2C, 2F, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (61) 2B, 2C, 2F, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (62) 2B, 2C, 2F, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (63) 2B, 2C, 2F, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (64) 2B, 2C, 2F, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (65) 2B, 2C, 2F, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (66) 2B, 2C, 2F, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (67) 1C, 1G, 1I, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (68) 1C, 1G, 1I, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (69) 1C, 1H, 1, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (70) 1C, 1H, 1, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (71) 1C, 1D, 1J, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (72) 1C, 1D, 1J, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (73) 1C, 1D, 1K, 1L, 1M, and 1F. In some embodiments, the butadiene pathway includes (74) 1C, 1D, 1K, 1L, 1N, and 1F. In some embodiments, the butadiene pathway includes (75) 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (76) 2C, 2R, 2S, 2E, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (77) 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (78) 2C, 2R, 2S, 2E, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (79) 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (80) 2C, 2R, 2S, 2E, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (81) 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (82) 2C, 2R, 2S, 2E, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (83) 2C, 2R, 2S, 2E, 2G, 2, and 2I. In some embodiments, the butadiene pathway includes (84) 2C, 2D, 2E, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (85) 2C, 2D, 2E, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (86) 2C, 2D, 2E, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (87) 2C, 2D, 2E, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (88) 2C, 2D, 2E, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (89) 2C, 2D, 2E, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (90) 2C, 2D, 2E, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (91) 2C, 2D, 2E, 2G, 2N, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (92) 2C, 2F, 2J, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (93) 2C, 2F, 2J, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (94) 2C, 2F, 2K, 2L, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (95) 2C, 2F, 2K, 2L, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (96) 2C, 2F, 2G, 2M, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (97) 2C, 2F, 2G, 2M, 2O, 2P, and 2I. In some embodiments, the butadiene pathway includes (98) 2C, 2F, 2G, 2N, 2O, 2Q, and 2I. In some embodiments, the butadiene pathway includes (99) 2C, 2F, 2G, 2N, 2O, 2P, and 2I.

In some aspects of the invention, the microbial organism can include one, two, three, four, five, six, seven, eight, nine, ten, or eleven exogenous nucleic acids each encoding a butadiene pathway enzyme. In some aspects, the microbial organism includes exogenous nucleic acids encoding each of the enzymes of at least one of the pathways selected from (1)-(99). In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a 2,4-pentadienoate pathway, having at least one exogenous nucleic acid encoding a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce 2,4-pentadienoate, wherein the 2,4-pentadienoate pathway includes a pathway shown in FIGS. 1 and 2 selected from (1) 1A, 1B, 1C, 1G, 1I, 1L, and 1M; (2) 1A, 1B, 1C, 1G, 1I, 1L, and 1N; (3) 1A, 1B, 1C, 1H, 1I, 1L, and 1M; (4) 1A, 1B, 1C, 1H, 1I, 1L, and 1N; (5) 1A, 1B, 1C, 1D, 1J, 1L, and 1M; (6) 1A, 1B, 1C, 1D, 1J, 1L, and 1N; (7) 1A, 1B, 1C, 1D, 1K, 1L, and 1M; (8) 1A, 1B, 1C, 1D, 1K, 1L, and 1N; (9) 1B, 1C, 1G, 1I, 1L, and 1M; (10) 1B, 1C, 1G, 1I, 1L, and 1N; (11) 1B, 1C, 1I, 1,1L, and 1M; (12) 1B, 1C, 1H, 1I, 1L, and 1N; (13) 1B, 1C, 1D, 1J, 1L, and 1M; (14) 1B, 1C, 1D, 1J, 1L, and 1N; (15) 1B, 1C, 1D, 1K, 1L, and 1M; (16) 1B, 1C, 1D, 1K, 1L, and 1N; (17) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2Q; (18) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2P; (19) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2Q; (20) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2P; (21) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2Q; (22) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2P; (23) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2Q; (24) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2P; (25) 2A, 2B, 2C, 2R, 2S, 2E, 2G, and 2H; (26) 2A, 2B, 2C, 2D, 2E, 2J, 2L, 2O, and 2Q; (27) 2A, 2B, 2C, 2D, 2E; 2J, 2L, 2O, and 2P; (28) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2Q; (29) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2P; (30) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2Q; (31) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2P; (32) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2Q; (33) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2P; (34) 2A, 2B, 2C, 2F, 2J, 2L, 2O, and 2Q; (35) 2A, 2B, 2C, 2F, 2J, 2L, 2O, and 2P; (36) 2A, 2B, 2C, 2F, 2K, 2L, 2O, and 2Q; (37) 2A, 2B, 2C, 2F, 2K, 2L, 2O, and 2P; (38) 2A, 2B, 2C, 2F, 2G, 2M, 2O, and 2Q; (39) 2A, 2B, 2C, 2F, 2G, 2M, 2O, and 2P; (40) 2A, 2B, 2C, 2F, 2G, 2N, 2O, and 2Q; (41) 2A, 2B, 2C, 2F, 2G, 2N, 2O, and 2P; (42) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2Q; (43) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2P; (44) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2Q; (45) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2P; (46) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2Q; (47) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2P; (48) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2Q; (49) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2P; (50) 2B, 2C, 2R, 2S, 2E, 2G, and 2H; (51) 2B, 2C, 2D, 2E, 2J, 2L, 2O, and 2Q; (52) 2B, 2C, 2D, 2E, 2J, 2L, 2O, and 2P; (53) 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2Q; (54) 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2P; (55) 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2Q; (56) 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2P; (57) 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2Q; (58) 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2P; (59) 2B, 2C, 2F, 2J, 2 L, 2O, and 2Q; (60) 2B, 2C, 2F, 2J, 2L, 2O, and 2P; (61) 2B, 2C, 2F, 2K, 2L, 2O, and 2Q; (62) 2B, 2C, 2F, 2K, 2L, 2O, and 2P; (63) 2B, 2C, 2F, 2G, 2M, 2O, and 2Q; (64) 2B, 2C, 2F, 2G, 2M, 2O, and 2P; (65) 2B, 2C, 2F, 2G, 2N, 2O, and 2Q; (66) 2B, 2C, 2F, 2G, 2N, 2O, and 2P; (67) 1C, 1G, 1I, 1L, and 1M; (68) 1C, 1G, 1I, 1L, and 1N; (69) 1C, 1H, 1I, 1L, and 1M; (70) 1C, 1H, 1I, 1L, and 1N; (71) 1C, 1D, 1J, 1L, and 1M; (72) 1C, 1D, 1J, 1L, and 1N; (73) 1C, 1D, 1K, 1L, and 1M; (74) 1C, 1D, 1K, 1L, and 1N; (75) 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2Q; (76) 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2P; (77) 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2Q; (78) 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2P; (79) 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2Q; (80) 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2P; (81) 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2Q; (82) 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2P; (83) 2C, 2R, 2S, 2E, 2G, and 2H; (84) 2C, 2D, 2E, 2J, 2L, 2O, and 2Q; (85) 2C, 2D, 2E, 2J, 2L, 2O, and 2P; (86) 2C, 2D, 2E, 2K, 2L, 2O, and 2Q; (87) 2C, 2D, 2E, 2K, 2L, 2O, and 2P; (88) 2C, 2D, 2E, 2G, 2M, 2O, and 2Q; (89) 2C, 2D, 2E, 2G, 2M, 2O, and 2P; (90) 2C, 2D, 2E, 2G, 2N, 2O, and 2Q; (91) 2C, 2D, 2E, 2G, 2N, 2O, and 2P; (92) 2C, 2F, 2J, 2L, 2O, and 2Q; (93) 2C, 2F, 2J, 2L, 2O, and 2P; (94) 2C, 2F, 2K, 2L, 2O, and 2Q; (95) 2C, 2F, 2K, 2L, 2O, and 2P; (96) 2C, 2F, 2G, 2M, 2O, and 2Q; (97) 2C, 2F, 2G, 2M, 2O, and 2P; (98) 2C, 2F, 2G, 2N, 2O, and 2Q; and (99) 2C, 2F, 2G, 2N, 2O, and 2P, wherein 1A is an acetaldehyde dehydrogenase, wherein 1B is a 4-hydroxy 2-oxovalerate aldolase, wherein 1C is a 4-hydroxy 2-oxovalerate dehydratase, wherein 1D is a 2-oxopentenoate reductase, wherein 1E is a 2-hydroxypentenoate dehydratase, wherein 1G is a 2-oxopentenoate ligase, wherein 1H is a 2-oxopentenoate:acetyl CoA CoA transferase, wherein 1I is a 2-oxopentenoyl-CoA reductase, wherein 1J is a 2-hydroxypentenoate ligase, wherein 1K is a 2-hydroxypentenoate:acetyl-CoA CoA transferase, wherein 1L is a 2-hydroxypentenoyl-CoA dehydratase, wherein 1M is a 2,4-Pentadienoyl-CoA hydrolase, wherein 1N is a 2,4-Pentadienoyl-CoA:acetyl CoA CoA transferase, wherein 2A is an acetyl-CoA carboxylase, wherein 2B is a malonyl-CoA:acetyl-CoA acyltransferase, wherein 2C is a 3-Oxoglutaryl-CoA reductase (ketone-reducing), wherein 2D is a 3-hydroxyglutaryl-CoA reductase (aldehyde forming), wherein 2E is a 3-hydroxy-5-oxopentanoate reductase, wherein 2F is a 3-hydroxyglutaryl-CoA reductase (alcohol forming), wherein 2G is a 3,5-dihydroxypentanoate dehydratase, wherein 2H is a 5-hydroxypent-2-enoate dehydratase, wherein 2J is a 3,5-dihydroxypentanoate ligase, wherein 2K is a 3,5-dihydroxypentanoate:acetyl-CoA CoA transferase, wherein 2L is a 3,5-dihydroxypentanoyl-CoA dehydratase, wherein 2M is a 5-hydroxypent-2-enoate ligase, wherein 2N is a 5-hydroxypent-2-enoate:acetyl-CoA CoA transferase, wherein 2O is a 5-hydroxypent-2-enoyl-CoA hydrolase, wherein 2P is a 2,4-pentadienoyl-CoA CoA hydrolase, wherein 2Q is a 2,4-pentadienoyl-CoA:acetyl-CoA CoA transferase, wherein 2R is a Phosphate-3-hydroxyglutaryl transferase, and wherein 2S is a 3-hydroxy-5-oxopentanoate synthase.

In some embodiments, the 2,4-pentadienoate pathway comprises (1) 1A, 1B, 1C, 1G, 1I, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (2) 1A, 1B, 1C, 1G, 1I, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (3) A, 1B, 1C, 1H, 1, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (4) 1A, 1B, 1C, 1H, 1I, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (5) 1A, 1B, 1C, 1D, 1J, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (6) 1A, 1B, 1C, 1D, 1J, 1L, and N. In some embodiments, the 2,4-pentadienoate pathway comprises (7) 1A, 1B, 1C, 1D, 1K, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (8) 1A, 1B, 1C, 1D, 1K, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (9) 1B, 1C, 1G, 1I, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (10) 1B, 1C, 1G, 1, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (11) 1B, 1C, 1H, 1I, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (12) 1B, 1C, 1H, 1I, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (13) 1B, 1C, 1D, 1J, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (14) 1B, 1C, 1D, 1J, 1L, and N. In some embodiments, the 2,4-pentadienoate pathway comprises (15) 1B, 1C, 1D, 1K, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (16) 1B, 1C, 1D, 1K, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (17) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (18) 2A, 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (19) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (20) 2A, 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (21) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (22) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (23) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (24) 2A, 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (25) 2A, 2B, 2C, 2R, 2S, 2E, 2G, and 2H. In some embodiments, the 2,4-pentadienoate pathway comprises (26) 2A, 2B, 2C, 2D, 2E, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (27) 2A, 2B, 2C, 2D, 2E; 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (28) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (29) 2A, 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (30) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (31) 2A, 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (32) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (33) 2A, 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (34) 2A, 2B, 2C, 2F, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (35) 2A, 2B, 2C, 2F, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (36) 2A, 2B, 2C, 2F, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (37) 2A, 2B, 2C, 2F, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (38) 2A, 2B, 2C, 2F, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (39) 2A, 2B, 2C, 2F, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (40) 2A, 2B, 2C, 2F, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (41) 2A, 2B, 2C, 2F, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (42) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (43) 2B, 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (44) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (45) 2B, 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (46) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (47) 2B, 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (48) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (49) 2B, 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (50) 2B, 2C, 2R, 2S, 2E, 2G, and 2H. In some embodiments, the 2,4-pentadienoate pathway comprises (51) 2B, 2C, 2D, 2E, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (52) 2B, 2C, 2D, 2E, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (53) 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (54) 2B, 2C, 2D, 2E, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (55) 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (56) 2B, 2C, 2D, 2E, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (57) 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (58) 2B, 2C, 2D, 2E, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (59) 2B, 2C, 2F, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (60) 2B, 2C, 2F, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (61) 2B, 2C, 2F, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (62) 2B, 2C, 2F, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (63) 2B, 2C, 2F, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (64) 2B, 2C, 2F, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (65) 2B, 2C, 2F, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (66) 2B, 2C, 2F, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (67) 1C, 1G, 1I, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (68) 1C, 1G, 1I, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (69) 1C, 1H, 1I, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (70) 1C, 1H, 1I, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (71) C, 1D, 1J, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (72) 1C, 1D, 1J, 1L, and 1N. In some embodiments, the 2,4-pentadienoate pathway comprises (73) 1C, 1D, 1K, 1L, and 1M. In some embodiments, the 2,4-pentadienoate pathway comprises (74) 1C, 1D, 1K, 1L, and N. In some embodiments, the 2,4-pentadienoate pathway comprises (75) 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (76) 2C, 2R, 2S, 2E, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (77) 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (78) 2C, 2R, 2S, 2E, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (79) 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (80) 2C, 2R, 2S, 2E, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (81) 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (82) 2C, 2R, 2S, 2E, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (83) 2C, 2R, 2S, 2E, 2G, and 2H. In some embodiments, the 2,4-pentadienoate pathway comprises (84) 2C, 2D, 2E, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (85) 2C, 2D, 2E, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (86) 2C, 2D, 2E, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (87) 2C, 2D, 2E, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (88) 2C, 2D, 2E, 2G, .2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (89) 2C, 2D, 2E, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (90) 2C, 2D, 2E, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (91) 2C, 2D, 2E, 2G, 2N, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (92) 2C, 2F, 2J, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (93) 2C, 2F, 2J, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (94) 2C, 2F, 2K, 2L, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (95) 2C, 2F, 2K, 2L, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (96) 2C, 2F, 2G, 2M, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (97) 2C, 2F, 2G, 2M, 2O, and 2P. In some embodiments, the 2,4-pentadienoate pathway comprises (98) 2C, 2F, 2G, 2N, 2O, and 2Q. In some embodiments, the 2,4-pentadienoate pathway comprises (99) 2C, 2F, 2G, 2N, 2O, and 2P.

In some aspects of the invention, the microbial organism can include one, two, three, four, five, six, seven, eight, nine, or ten exogenous nucleic acids each encoding a 2,4-pentadienoate pathway enzyme. In some aspects, the microbial organism includes exogenous nucleic acids encoding each of the enzymes of at least one of the pathways selected from (1)-(99). In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme or a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate, wherein the butadiene pathway or the 2,4-pentadienoate pathway includes a pathway as described above, further having an acetyl-CoA pathway having a pathway shown in FIG. 3 selected from: (1) 3T and 3V; (2) 3T, 3W, and 3X; (3) 3U and 3V; (4) 3U, 3W, and 3X, wherein 3T is a fuctose-6-phosphate phosphoketolase, wherein 3U is a xylulose-5-phosphate phosphoketolase, wherein 3V is a phosphotransacetylase, wherein 3W is an acetate kinase, wherein 3X is an acetyl-CoA transferase, an acetyl-CoA synthetase, or an acetyl-CoA ligase. In some embodiments, the acetyl-CoA pathway comprises (1) 3T and 3V. In some embodiments, the acetyl-CoA pathway comprises (2) 3T, 3W, and 3X. In some embodiments, the acetyl-CoA pathway comprises (3) 3U and 3V. In some embodiments, the acetyl-CoA pathway comprises (4) 3U, 3W, and 3X.

In some aspects, the microbial organism has an acetyl-CoA pathway as described above wherein an enzyme of the acetyl-CoA pathway is encoded by at least one exogenous nucleic acid and is expressed in a sufficient amount to enhance carbon flux through acetyl-CoA. In some aspects, the microbial organism has one, two, or three exogenous nucleic acids each encoding an acetyl-CoA pathway enzyme. In some aspects, the microbial organism has exogenous nucleic acids encoding each of the enzymes of at least one of the acetyl-CoA pathways described above selected from (1)-(4). In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme or a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate, wherein the butadiene pathway or the 2,4-pentadienoate pathway includes a pathway as described above, further having a formaldehyde fixation pathway as shown in FIG. 3 selected from: (1) 3D and 3Z; (2) 3D; or (3) 3B and 3C, wherein 3B is a 3-hexulose-6-phosphate synthase, wherein 3C is a 6-phospho-3-hexuloisomerase, wherein 3D is a dihydroxyacetone synthase, wherein 3Z is a fructose-6-phosphate aldolase. In some embodiments, the formaldehyde fixation pathway comprises (1) 3D and 3Z. In some embodiments, the formaldehyde fixation pathway comprises (2) 3D. In some embodiments, the formaldehyde fixation pathway comprises (3) 3B and 3C.

In some aspects, the microbial organism has a formaldehyde fixation pathway as described above wherein an enzyme of the formaldehyde fixation pathway is encoded by at least one exogenous nucleic acid and is expressed in a sufficient amount to enhance carbon flux through acetyl-CoA. In some aspects, the microbial organism has one or two exogenous nucleic acids each encoding a formaldehyde fixation pathway enzyme. In some aspects, the microbial organism has exogenous nucleic acids encoding each of the enzymes of at least one of the formaldehyde fixation pathways described above selected from (1)-(3). In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme or a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate, wherein the butadiene pathway or 2,4-pentadienoate pathway includes a pathway as described above, further having a methanol metabolic pathway as shown in FIG. 4 selected from (1) 4A and 4B; (2) 4A, 4B and 4C; (3) 4J; (4) 4J, 4K and 4C; (5) 4J, 4M, and 4N; (6) 4J and 4L; (7) 4J, 4L, and 4G; (8) 4J, 4L, and 4I; (9) 4A, 4B, 4C, 4D, and 4E; (10) 4A, 4B, 4C, 4D, and 4F; (11) 4J, 4K, 4C, 4D, and 4E; (12) 4J, 4K, 4C, 4D, and 4F; (13) 4J, 4M, 4N, and 4O; (14) 4A, 4B, 4C, 4D, 4E, and 4G; (15) 4A, 4B, 4C, 4D, 4F, and 4G; (16) 4J, 4K, 4C, 4D, 4E, and 4G; (17) 4J, 4K, 4C, 4D, 4F, and 4G; (18) 4J, 4M, 4N, 4O, and 4G; (19) 4A, 4B, 4C, 4D, 4E, and 4I; (20) 4A, 4B, 4C, 4D, 4F, and 4I; (21) 4J, 4K, 4C, 4D, 4E, and 4I; (22) 4J, 4K, 4C, 4D, 4F, and 4I; and (23) 4J, 4M, 4N, 4O, and 4I, wherein 4A is a methanol methyltransferase, wherein 4B is a methylenetetrahydrofolate reductase, wherein 4C is a methylenetetrahydrofolate dehydrogenase, wherein 4D is a methenyltetrahydrofolate cyclohydrolase, wherein 4E is a formyltetrahydrofolate deformylase, wherein 4F is a formyltetrahydrofolate synthetase, wherein 4G is a formate hydrogen lyase, wherein 4I is a formate dehydrogenase, wherein 4J is a methanol dehydrogenase, wherein 4K is a formaldehyde activating enzyme or spontaneous, wherein 4L is a formaldehyde dehydrogenase, wherein 4M is a S-(hydroxymethyl)glutathione synthase or spontaneous, wherein 4N is a glutathione-dependent formaldehyde dehydrogenase, wherein 4O is a S-formylglutathione hydrolase. In some embodiments, the methanol metabolic pathway comprises (1) 4A and 4B. In some embodiments, the methanol metabolic pathway comprises (2) 4A, 4B and 4C. In some embodiments, the methanol metabolic pathway comprises (3) 4J, 4K and 4C. In some embodiments, the methanol metabolic pathway comprises (4) 4J, 4M, and 4N. In some embodiments, the methanol metabolic pathway comprises (5) 4J and 4L. In some embodiments, the methanol metabolic pathway comprises (6) 4J, 4L, and 4G. In some embodiments, the methanol metabolic pathway comprises (7) 4J, 4L, and 4I. In some embodiments, the methanol metabolic pathway comprises (8) 4A, 4B, 4C, 4D, and 4E. In some embodiments, the methanol metabolic pathway comprises (9) 4A, 4B, 4C, 4D, and 4F. In some embodiments, the methanol metabolic pathway comprises (10) 4J, 4K, 4C, 4D, and 4E. In some embodiments, the methanol metabolic pathway comprises (11) 4J, 4K, 4C, 4D, and 4F. In some embodiments, the methanol metabolic pathway comprises (12) 4J, 4M, 4N, and 40. In some embodiments, the methanol metabolic pathway comprises (13) 4A, 4B, 4C, 4D, 4E, and 4G; In some embodiments, the methanol metabolic pathway comprises (14) 4A, 4B, 4C, 4D, 4F, and 4G. In some embodiments, the methanol metabolic pathway comprises (15) 4J, 4K, 4C, 4D, 4E, and 4G. In some embodiments, the methanol metabolic pathway comprises (16) 4J, 4K, 4C, 4D, 4F, and 4G. In some embodiments, the methanol metabolic pathway comprises (17) 4J, 4M, 4N, 4O, and 4G. In some embodiments, the methanol metabolic pathway comprises (18) 4A, 4B, 4C, 4D, 4E, and 4I. In some embodiments, the methanol metabolic pathway comprises (19) 4A, 4B, 4C, 4D, 4F, and 4I. In some embodiments, the methanol metabolic pathway comprises (20) 4J, 4K, 4C, 4D, 4E, and 4I. In some embodiments, the methanol metabolic pathway comprises (21) 4J, 4K, 4C, 4D, 4F, and 4I. In some embodiments, the methanol metabolic pathway comprises (22) 4J, 4M, 4N, 4O, and 4I.

In some aspects, the microbial organism has a methanol metabolic pathway as described above wherein an enzyme of the methanol metabolic pathway is encoded by at least one exogenous nucleic acid. In some aspects, the microbial organism has one, two, three, four, five, or six exogenous nucleic acids each encoding a methanol metabolic pathway enzyme. In some aspects, the microbial organism has exogenous nucleic acids encoding each of the enzymes of at least one of the methanol metabolic pathways described above selected from (1)-(23). In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme or a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or a 2,4-pentadienoate, wherein the butadiene pathway or the 2,4-pentadienoate pathway includes a pathway as described above, further having a formate assimilation pathway as shown in FIG. 3 selected from: (1) 3E; (2) 3F, and 3G; (3) 3H, 3I, 3J, and 3K; (4) 3H, 3I, 3J, 3L, 3M, and 3N; (5) 3E, 3H, 3I, 3J, 3L, 3M, and 3N; (6) 3F, 3G, 3H, 3I, 3J, 3L, 3M, and 3N; (7), 3H, 31I, 3J, 3L, 3M, and 3N; and (8) 3H, 3I, 3J, 3O, and 3P, wherein 3E is a formate reductase, 3F is a formate ligase, a formate transferase, or a formate synthetase, wherein 3G is a formyl-CoA reductase, wherein 3H is a formyltetrahydrofolate synthetase, wherein 31 is a methenyltetrahydrofolate cyclohydrolase, wherein 3J is a methylenetetrahydrofolate dehydrogenase, wherein 3K is a formaldehyde-forming enzyme or spontaneous, wherein 3L is a glycine cleavage system, wherein 3M is a serine hydroxymethyltransferase, wherein 3N is a serine deaminase, wherein 3O is a methylenetetrahydrofolate reductase, wherein 3P is an acetyl-CoA synthase. In some embodiments, the formate assimilation pathway comprises (1) 3E. In some embodiments, the formate assimilation pathway comprises (2) 3F, and 3G. In some embodiments, the formate assimilation pathway comprises (3) 3H, 3I, 3J, and 3K. In some embodiments, the formate assimilation pathway comprises (4) 3H, 3I, 3J, 3L, 3M, and 3N. In some embodiments, the formate assimilation pathway comprises (5) 3E, 3H, 3I, 3J, 3L, 3M, and 3N. In some embodiments, the formate assimilation pathway comprises (6) 3F, 3G, 3H, 3I, 3J, 3L, 3M, and 3N. In some embodiments, the formate assimilation pathway comprises (7) 3K, 3H, 3I, 3J, 3L, 3M, and 3N. In some embodiments, the formate assimilation pathway comprises (8) 3H, 3I, 3J, 3O, and 3P.

In some aspects, the microbial organism has a formate assimilation pathway as described above wherein an enzyme of the formate assimilation pathway is encoded by at least one exogenous nucleic acid and is expressed in a sufficient amount to enhance carbon flux through acetyl-CoA. In some aspects, the microbial organism has one, two, three, four, five, six, seven or eight exogenous nucleic acids each encoding a formate assimilation pathway enzyme. In some aspects, the microbial organism has exogenous nucleic acids encoding each of the enzymes of at least one of the formate assimilation pathways described above selected from (1)-(8). In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some aspects, the formate assimilation pathway as described above further includes: (1) 3Q; (2) 3R and 3S; (3) 3Y and 3Q; or (4) 3Y, 3R, and 3S, wherein 3Q is a pyruvate formate lyase, wherein 3R is a pyruvate dehydrogenase, a pyruvate ferredoxin oxidoreductase, or a pyruvate:NADP+ oxidoreductase, wherein 3S is a formate dehydrogenase, wherein 3Y is a glyceraldehyde-3-phosphate dehydrogenase or an enzyme of lower glycolysis. In some aspects, the formate assimilation pathway as described above further includes (1) 3Q. In some aspects, the formate assimilation pathway as described above further includes (2) 3R and 3S. In some aspects, the formate assimilation pathway as described above further includes (3) 3Y and 3Q. In some aspects, the formate assimilation pathway as described above further includes (4) 3Y, 3R, and 3S.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme or a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate, wherein the butadiene pathway or the 2,4-pentadienoate pathway includes a pathway as described above, further having a methanol oxidation pathway having a methanol dehydrogenase as shown in FIG. 3. In some aspects, the microbial organism has at least one exogenous nucleic acid encoding a methanol oxidation pathway enzyme expressed in a sufficient amount to produce formaldehyde in the presence of methanol. In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway having at least one exogenous nucleic acid encoding a butadiene pathway enzyme or a 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce butadiene or 2,4-pentadienoate, wherein the butadiene pathway or 2,4-pentadienoate pathway includes a pathway as described above, further having a hydrogenase or carbon monoxide dehydrogenase. In some aspects, the microbial organism has at least one exogenous nucleic acid encoding the hydrogenase or the carbon monoxide dehydrogenase. In some aspects, the at least one exogenous nucleic acid is a heterologous nucleic acid. In some aspects, the non-naturally occurring microbial organism is in a substantially anaerobic culture medium.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway as described herein, wherein the microbial organism further includes attenuation of one or more endogenous enzymes, which enhances carbon flux through acetyl-CoA. For example, in some aspects, the endogenous enzyme can be selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof. Accordingly, in some aspects, the attenuation is of the endogenous enzyme DHA kinase. In some aspects, the attenuation is of the endogenous enzyme methanol oxidase. In some aspects, the attenuation is of the endogenous enzyme PQQ-dependent methanol dehydrogenase. In some aspects, the attenuation is of the endogenous enzyme DHA synthase. The invention also provides a microbial organism wherein attenuation is of any combination of two or three endogenous enzymes described herein. For example, a microbial organism of the invention can include attenuation of DHA kinase and DHA synthase, or alternatively methanol oxidase and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and DHA synthase. The invention also provides a microbial organism wherein attenuation is of all endogenous enzymes described herein. For example, in some aspects, a microbial organism described herein includes attenuation of DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase and DHA synthase.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway as described herein, wherein the microbial organism further includes attenuation of one or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway. Examples of these endogenous enzymes are disclosed in FIG. 3. It is understood that a person skilled in the art would be able to readily identify enzymes of such competing pathways. Competing pathways can be dependent upon the host microbial organism and/or the exogenous nucleic acid introduced into the microbial organism as described herein. Accordingly, in some aspects of the invention, the microbial organism includes attenuation of one, two, three, four, five, six, seven, eight, nine, ten or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway as described herein, wherein the microbial organism further includes a gene disruption of one or more endogenous nucleic acids encoding enzymes, which enhances carbon flux through acetyl-CoA. For example, in some aspects, the endogenous enzyme can be selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof. According, in some aspects, the gene disruptiondisruption is of an endogenous nucleic acid encoding the enzyme DHA kinase. In some aspects, the gene disruptiondisruption is of an endogenous nucleic acid encoding the enzyme methanol oxidase. In some aspects, the gene disruptiondisruption is of an endogenous nucleic acid encoding the enzyme PQQ-dependent methanol dehydrogenase. In some aspects, the gene disruption is of an endogenous nucleic acid encoding the enzyme DHA synthase. The invention also provides a microbial organism wherein the gene disruption is of any combination of two or three nucleic acids encoding endogenous enzymes described herein. For example, a microbial organism of the invention can include a gene disruption of DHA kinase and DHA synthase, or alternatively methanol oxidase and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and DHA synthase. The invention also provides a microbial organism wherein all endogenous nucleic acids encoding enzymes described herein are disrupted. For example, in some aspects, a microbial organism described herein includes disruption of DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase and DHA synthase.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate as described herein, wherein the microbial organism further includes a gene disruption of one or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway. Examples of these endogenous enzymes are disclosed in FIG. 3. It is understood that a person skilled in the art would be able to readily identify enzymes of such competing pathways. Competing pathways can be dependent upon the host microbial organism and/or the exogenous nucleic acid introduced into the microbial organism as described herein. Accordingly, in some aspects of the invention, the microbial organism includes a gene disruption of one, two, three, four, five, six, seven, eight, nine, ten or more endogenous nucleic acids encoding enzymes of a competing formaldehyde assimilation or dissimilation pathway.

In some embodiments, the invention provides a non-naturally occurring microbial organism having a butadiene pathway or a 2,4-pentadienoate pathway as described herein, further having a hydrogen synthesis pathway catalyzing the synthesis of hydrogen from a reducing equivalent, said hydrogen synthesis pathway including an enzyme selected from the group consisting: a hydrogenase, a formate-hydrogene lyase, and ferredoxin: NADP+ oxidoreductase. In some aspects, the reducing equivalent is selected from the group consisting of NADH, NADPH, FADH, reduced quinones, reduced ferredoxins, reduced flavodoxins and reduced thioredoxins. In some aspects, the non-naturally occurring microbial organism has at least one exogenous nucleic acid encoding a hydrogen synthesis pathway enzyme expressed in a sufficient amount to produce hydrogen.

In an additional embodiment, the invention provides a non-naturally occurring microbial organism having a butadiene or 2,4-pentadienoate pathway, wherein the non-naturally occurring microbial organism has at least one exogenous nucleic acid encoding an enzyme or protein that converts a substrate to a product selected from the group consisting of acetyl CoA to acetaldehyde, pyruvate to 4-hydroxy 2-oxovalerate, 4-hydroxy 2-oxovalerate to 2-oxopentenoate, 2-oxopentenoate to 2-oxopentenoyl-CoA, 2-oxopentenoyl-CoA to 2-hydroxypentenoyl-CoA, 2-hydroxypentenoyl-CoA to 2,4-Pentadienoyl-CoA, 2,4-Pentadienoyl-CoA to 2,4-pentadienoate, 2-oxopentenoate to 2-hydroxypentenoate, 2-hydroxypentenoatet to 2,4-pentadienoate, 2-hydroxypentenoate to 2-hydroxypentenoyl-CoA, acetyl-CoA to malonyl-CoA, malonyl-CoA to 3-Oxoglutaryl-CoA, 3-Oxoglutaryl-CoA to 3-hydroxyglutaryl-CoA, 3-hydroxyglutaryl-CoA to 3-hydroxyglutaryl-phosphate, 3-hydroxyglutaryl-CoA to 3-hydroxy-5-oxopentanoate, 3-hydroxyglutaryl-CoA to 3-hydroxy-5-oxopentanoate, 3-hydroxy-5-oxopentanoate to 3,5-dihydroxypentanoate, 3-hydroxyglutaryl-CoA to 3,5-dihydroxypentanoate, 3,5-dihydroxypentanoate to 3,5-dihydroxypentanoyl-CoA, 3,5-dihydroxypentanoyl-CoA to 5-hydroxypent-2-enoyl-CoA, 5-hydroxypent-2-enoyl-CoA to 2,4-pentadienoyl-CoA, 2,4-pentadienoyl-CoA to 2,4-pentadienoate, 3,5-dihydroxypentanoate to 5-hydroxypent-2-enoate, 5-hydroxypent-2-enoate to 2,4-pentadienoate, 5-hydroxypent-2-enoate to 5-hydroxypent-2-enoyl-CoA, 2,4-pentadienoate to butadiene. One skilled in the art will understand that these are merely exemplary and that any of the substrate-product pairs disclosed herein suitable to produce a desired product and for which an appropriate activity is available for the conversion of the substrate to the product can be readily determined by one skilled in the art based on the teachings herein. Thus, the invention provides a non-naturally occurring microbial organism containing at least one exogenous nucleic acid encoding an enzyme or protein, where the enzyme or protein converts the substrates and products of a butadiene or 2,4-pentadienoate pathway, such as that shown in FIGS. 1 and 2.

While generally described herein as a microbial organism that contains a butadiene or 2,4-pentadienoate pathway, it is understood that the invention additionally provides anon-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a butadiene or 2,4-pentadienoate pathway enzyme expressed in a sufficient amount to produce an intermediate of a butadiene or 2,4-pentadienoate pathway. For example, as disclosed herein, a butadiene or 2,4-pentadienoate pathway is exemplified in FIGS. 1-2. Therefore, in addition to a microbial organism containing a butadiene or 2,4-pentadienoate pathway that produces butadiene or 2,4-pentadienoate, the invention additionally provides a non-naturally occurring microbial organism comprising at least one exogenous nucleic acid encoding a butadiene or 2,4-pentadienoate pathway enzyme, where the microbial organism produces a butadiene or 2,4-pentadienoate pathway intermediate, for example, 4-hydroxy-2-oxovalerate, 2-oxopentenoate, 2-oxopentenoyl-CoA, 2-hydroxypentenoyl-CoA, 2,4-Pentadienoyl-CoA, 2-hydroxypentenoate, malonyl-CoA, 3-Oxoglutaryl-CoA, 3-hydroxyglutaryl-CoA, 3-hydroxyglutaryl-phosphate, 3-hydroxy-5-oxopentanoate, 3,5-dihydroxypentanoate, 3,5-dihydroxypentanoyl-CoA, 5-hydroxypent-2-enoyl-CoA, 2,4-pentadienoyl-CoA, 3,5-dihydroxypentanoate, or 5-hydroxypent-2-enoate.

It is understood that any of the pathways disclosed herein, as described in the Examples and exemplified in the Figures, including the pathways of FIGS. 1-4, can be utilized to generate a non-naturally occurring microbial organism that produces any pathway intermediate or product, as desired. As disclosed herein, such a microbial organism that produces an intermediate can be used in combination with another microbial organism expressing downstream pathway enzymes to produce a desired product. However, it is understood that a non-naturally occurring microbial organism that produces a butadiene or 2,4-pentadienoate pathway intermediate can be utilized to produce the intermediate as a desired product.

The invention is described herein with general reference to the metabolic reaction, reactant or product thereof, or with specific reference to one or more nucleic acids or genes encoding an enzyme associated with or catalyzing, or a protein associated with, the referenced metabolic reaction, reactant or product. Unless otherwise expressly stated herein, those skilled in the art will understand that reference to a reaction also constitutes reference to the reactants and products of the reaction. Similarly, unless otherwise expressly stated herein, reference to a reactant or product also references the reaction, and reference to any of these metabolic constituents also references the gene or genes encoding the enzymes that catalyze or proteins involved in the referenced reaction, reactant or product. Likewise, given the well known fields of metabolic biochemistry, enzymology and genomics, reference herein to a gene or encoding nucleic acid also constitutes a reference to the corresponding encoded enzyme and the reaction it catalyzes or a protein associated with the reaction as well as the reactants and products of the reaction.

As disclosed herein, the product 2,4-pentadienoate and intermediates pyruvate, 4-hydroxy-2-oxovalerate, 2-oxopentenoate, 2-hydroxypentenoate, 3-hydroxyglutaryl-phosphate, 3-hydroxy-5-oxopentanoate, 3,5-dihydroxypentanoate, or 5-hydroxypent-2-enoate, as well as other intermediates, are carboxylic acids, which can occur in various ionized forms, including fully protonated, partially protonated, and fully deprotonated forms. Accordingly, the suffix “-ate,” or the acid form, can be used interchangeably to describe both the free acid form as well as any deprotonated form, in particular since the ionized form is known to depend on the pH in which the compound is found. It is understood that carboxylate products or intermediates includes ester forms of carboxylate products or pathway intermediates, such as O-carboxylate and S-carboxylate esters. O- and S-carboxylates can include lower alkyl, that is C1 to C6, branched or straight chain carboxylates. Some such O- or S-carboxylates include, without limitation, methyl, ethyl, n-propyl, n-butyl, i-propyl, sec-butyl, and tert-butyl, pentyl, hexyl O- or S-carboxylates, any of which can further possess an unsaturation, providing for example, propenyl, butenyl, pentyl, and hexenyl O- or S-carboxylates. O-carboxylates can be the product of a biosynthetic pathway. Exemplary O-carboxylates accessed via biosynthetic pathways can include, without limitation, methyl 2,4-pentadienoate, ethyl 2,4-pentadienoate, and n-propyl2,4-pentadienoate. Other biosynthetically accessible O-carboxylates can include medium to long chain groups, that is C4-C22, O-carboxylate esters derived from fatty alcohols, such as butyl, pentanoyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl, lauryl, tridecyl, myristyl, pentadecyl, cetyl, palmitolyl, heptadecyl, stearyl, nonadecyl, arachidyl, heneicosyl, and behenyl alcohols, any one of which can be optionally branched and/or contain unsaturations. O-carboxylate esters can also be accessed via a biochemical or chemical process, such as esterification of a free carboxylic acid product or transesterification of an O- or S-carboxylate. S-carboxylates are exemplified by CoA S-esters, cysteinyl S-esters, alkylthioesters, and various aryl and heteroaryl thioesters.

The non-naturally occurring microbial organisms of the invention can be produced by introducing expressible nucleic acids encoding one or more of the enzymes or proteins participating in one or more butadiene or 2,4-pentadienoate biosynthetic pathways. Depending on the host microbial organism chosen for biosynthesis, nucleic acids for some or all of a particular butadiene or 2,4-pentadienoate biosynthetic pathway can be expressed. For example, if a chosen host is deficient in one or more enzymes or proteins for a desired biosynthetic pathway, then expressible nucleic acids for the deficient enzyme(s) or protein(s) are introduced into the host for subsequent exogenous expression. Alternatively, if the chosen host exhibits endogenous expression of some pathway genes, but is deficient in others, then an encoding nucleic acid is needed for the deficient enzyme(s) or protein(s) to achieve butadiene or 2,4-pentadienoate biosynthesis. Thus, a non-naturally occurring microbial organism of the invention can be produced by introducing exogenous enzyme or protein activities to obtain a desired biosynthetic pathway or a desired biosynthetic pathway can be obtained by introducing one or more exogenous enzyme or protein activities that, together with one or more endogenous enzymes or proteins, produces a desired product such as butadiene or 2,4-pentadienoate.

Host microbial organisms can be selected from, and the non-naturally occurring microbial organisms generated in, for example, bacteria, yeast, fungus or any of a variety of other microorganisms applicable or suitable to fermentation processes. Exemplary bacteria include any species selected from the order Enterobacteriales, family Enterobacteriaceae, including the genera Escherichia and Klebsiella; the order Aeromonadales, family Succinivibrionaceae, including the genus Anaerobiospirillum; the order Pasteurellales, family Pasteurellaceae, including the genera Actinobacillus and Mannheimia; the order Rhizobiales, family Bradyrhizobiaceae, including the genus Rhizobium; the order Bacillales, family Bacillaceae, including the genus Bacillus; the order Actinomycetales, families Corynebacteriaceae and Streptomycetaceae, including the genus Corynebacterium and the genus Streptomyces, respectively; order Rhodospirillales, family Acetobacteraceae, including the genus Gluconobacter; the order Sphingomonadales, family Sphingomonadaceae, including the genus Zymomonas; the order Lactobacillales, families Lactobacillaceae and Streptococcaceae, including the genus Lactobacillus and the genus Lactococcus, respectively; the order Clostridiales, family Clostridiaceae, genus Clostridium; and the order Pseudomonadales, family Pseudomonadaceae, including the genus Pseudomonas. Non-limiting species of host bacteria include Escherichia coli, Klebsiella oxytoca, Anaerobiospirillum succiniciproducens, Actinobacillus succinogenes, Mannheimia succiniciproducens, Rhizobium etli, Bacillus subtilis, Corynebacterium glutamicum, Gluconobacter oxydans, Zymomonas mobilis, Lactococcus lactis, Lactobacillus plantarum, Streptomyces coelicolor, Clostridium acetobutylicum, Pseudomonas fluorescens, and Pseudomonas putida.

Similarly, exemplary species of yeast or fingi species include any species selected from the order Saccharomycetales, family Saccaromycetaceae, including the genera Saccharomyces, Kluyveromyces and Pichia; the order Saccharomycetales, family Dipodascaceae, including the genus Yarrowia; the order Schizosaccharomycetales, family Schizosaccaromycetaceae, including the genus Schizosaccharomyces; the order Eurotiales, family Trichocomaceae, including the genus Aspergillus; and the order Mucorales, family Mucoraceae, including the genus Rhizopus. Non-limiting species of host yeast or fungi include Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Kluyveromyces marxianus, Aspergillus terreus, Aspergillus niger, Pichia pastoris, Rhizopus arrhizus, Rhizopus oryzae, Yarrowia lipolytica, and the like. E. coli is a particularly useful host organism since it is a well characterized microbial organism suitable for genetic engineering. Other particularly useful host organisms include yeast such as Saccharomyces cerevisiae. It is understood that any suitable microbial host organism can be used to introduce metabolic and/or genetic modifications to produce a desired product.

Depending on the butadiene or 2,4-pentadienoate biosynthetic pathway constituents of a selected host microbial organism, the non-naturally occurring microbial organisms of the invention will include at least one exogenously expressed butadiene or 2,4-pentadienoate pathway-encoding nucleic acid and up to all encoding nucleic acids for one or more butadiene or 2,4-pentadienoate biosynthetic pathways. For example, butadiene or 2,4-pentadienoate biosynthesis can be established in a host deficient in a pathway enzyme or protein through exogenous expression of the corresponding encoding nucleic acid. In a host deficient in all enzymes or proteins of a butadiene or 2,4-pentadienoate pathway, exogenous expression of all enzyme or proteins in the pathway can be included, although it is understood that all enzymes or proteins of a pathway can be expressed even if the host contains at least one of the pathway enzymes or proteins. For example, exogenous expression of all enzymes or proteins in a pathway for production of butadiene or 2,4-pentadienoate can be included, such as an acetaldehyde dehydrogenase, a 4-hydroxy 2-oxovalerate dehydratase, a 2-oxopentenoate reductase, 2-hydroxypentenoate:acetyl-CoA CoA transferase, 2-hydroxypentenoyl-CoA dehydratase, 2,4-Pentadienoyl-CoA hydrolase, and a 2,4-pentadienoate decarboxylase.

Given the teachings and guidance provided herein, those skilled in the art will understand that the number of encoding nucleic acids to introduce in an expressible form will, at least, parallel the butadiene or 2,4-pentadienoate pathway deficiencies of the selected host microbial organism. Therefore, a non-naturally occurring microbial organism of the invention can have one, two, three, four, five, six, seven, eight, nine, ten, or eleven, up to all nucleic acids encoding the enzymes or proteins constituting a butadiene or 2,4-pentadienoate biosynthetic pathway disclosed herein. In some embodiments, the non-naturally occurring microbial organisms also can include other genetic modifications that facilitate or optimize butadiene or 2,4-pentadienoate biosynthesis or that confer other useful functions onto the host microbial organism. One such other functionality can include, for example, augmentation of the synthesis of one or more of the butadiene or 2,4-pentadienoate pathway precursors such as acetyl-CoA, pyruvate, or malonyl-CoA.

Generally, a host microbial organism is selected such that it produces the precursor of a butadiene or 2,4-pentadienoate pathway, either as a naturally produced molecule or as an engineered product that either provides de novo production of a desired precursor or increased production of a precursor naturally produced by the host microbial organism. For example, acetyl-CoA, pyruvate, and malonyl-CoA are produced naturally in a host organism such as E. coli. A host organism can be engineered to increase production of a precursor, as disclosed herein. In addition, a microbial organism that has been engineered to produce a desired precursor can be used as a host organism and further engineered to express enzymes or proteins of a butadiene or 2,4-pentadienoate pathway.

In some embodiments, anon-naturally occurring microbial organism of the invention is generated from a host that contains the enzymatic capability to synthesize butadiene or 2,4-pentadienoate. In this specific embodiment it can be useful to increase the synthesis or accumulation of a butadiene or 2,4-pentadienoate pathway product to, for example, drive butadiene or 2,4-pentadienoate pathway reactions toward butadiene or 2,4-pentadienoate production. Increased synthesis or accumulation can be accomplished by, for example, overexpression of nucleic acids encoding one or more of the above-described butadiene or 2,4-pentadienoate pathway enzymes or proteins. Overexpression of the enzyme or enzymes and/or protein or proteins of the butadiene or 2,4-pentadienoate pathway can occur, for example, through modification of an endogenous gene to overexpress the gene, exogenous expression of the endogenous gene or genes, or through exogenous expression of the heterologous gene or genes. Therefore, naturally occurring organisms can be readily generated to be non-naturally occurring microbial organisms of the invention, for example, producing butadiene or 2,4-pentadienoate, through overexpression of one, two, three, four, five, six, seven, eight, nine, ten or eleven, that is, up to all nucleic acids encoding butadiene or 2,4-pentadienoate biosynthetic pathway enzymes or proteins. In addition, anon-naturally occurring organism can be generated by mutagenesis of an endogenous gene that results in an increase in activity of an enzyme in the butadiene or 2,4-pentadienoate biosynthetic pathway. For example, the promoter region of an endogenous gene can be modified to increase the expression of the gene.

In particularly useful embodiments, exogenous expression of the encoding nucleic acids is employed. Exogenous expression confers the ability to custom tailor the expression and/or regulatory elements to the host and application to achieve a desired expression level that is controlled by the user. However, endogenous expression also can be utilized in other embodiments such as by removing a negative regulatory effector or induction of the gene's promoter when linked to an inducible promoter or other regulatory element. Thus, an endogenous gene having a naturally occurring inducible promoter can be up-regulated by providing the appropriate inducing agent, or the regulatory region of an endogenous gene can be engineered to incorporate an inducible regulatory element, thereby allowing the regulation of increased expression of an endogenous gene at a desired time. Similarly, an inducible promoter can be included as a regulatory element for an exogenous gene introduced into a non-naturally occurring microbial organism.

It is understood that, in methods of the invention, any of the one or more exogenous nucleic acids can be introduced into a microbial organism to produce a non-naturally occurring microbial organism of the invention. The nucleic acids can be introduced so as to confer, for example, a butadiene or 2,4-pentadienoate biosynthetic pathway onto the microbial organism. Alternatively, encoding nucleic acids can be introduced to produce an intermediate microbial organism having the biosynthetic capability to catalyze some of the required reactions to confer butadiene or 2,4-pentadienoate biosynthetic capability. For example, a non-naturally occurring microbial organism having a butadiene or 2,4-pentadienoate biosynthetic pathway can comprise at least two exogenous nucleic acids encoding desired enzymes or proteins, such as the combination of 2-oxopentenoate ligase and 2,4-pentadienoate decarboxylase, or alternatively 5-hydroxypent-2-enoate dehydratase and 2,4-pentadienoate decarboxylase, or alternatively 2-hydroxypentenoate ligase and 2-hydroxypentenoyl-CoA dehydratase, or alternatively 2-hydroxypentenoate:acetyl-CoA CoA transferase and 2-hydroxypentenoyl-CoA dehydratase, or alternatively 3,5-dihydroxypentanoate ligase and 3,5-dihydroxypentanoyl-CoA dehydratase, or alternatively 3,5-dihydroxypentanoate:acetyl-CoA CoA transferase and 2-hydroxypentenoyl-CoA dehydratase, or alternatively 5-hydroxypent-2-enoate ligase and 5-hydroxypent-2-enoyl-CoA hydrolase, or alternatively 5-hydroxypent-2-enoate:acetyl-CoA CoA transferase and 5-hydroxypent-2-enoyl-CoA hydrolase, and the like. Thus, it is understood that any combination of two or more enzymes or proteins of a biosynthetic pathway can be included in a non-naturally occurring microbial organism of the invention. Similarly, it is understood that any combination of three or more enzymes or proteins of a biosynthetic pathway can be included in a non-naturally occurring microbial organism of the invention, for example, 2-oxopentenoate ligase, 2-oxopentenoyl-CoA reductase, and 2-hydroxypentenoyl-CoA dehydratase, or alternatively 2-hydroxypentenoate ligase, 2-hydroxypentenoyl-CoA dehydratase, and 2,4-Pentadienoyl-CoA hydrolase, or alternatively 3,5-dihydroxypentanoate ligase, 3,5-dihydroxypentanoyl-CoA dehydratase, 5-hydroxypent-2-enoyl-CoA hydrolase, or alternatively 5-hydroxypent-2-enoate ligase, 5-hydroxypent-2-enoyl-CoA hydrolase, and 2,4-pentadienoyl-CoA:acetyl-CoA CoA transferase, and so forth, as desired, so long as the combination of enzymes and/or proteins of the desired biosynthetic pathway results in production of the corresponding desired product. Similarly, any combination of four, five, six, seven, eight, nine, ten, eleven or more enzymes or proteins of a biosynthetic pathway as disclosed herein can be included in anon-naturally occurring microbial organism of the invention, as desired, so long as the combination of enzymes and/or proteins of the desired biosynthetic pathway results in production of the corresponding desired product.

In addition to the biosynthesis of butadiene or 2,4-pentadienoate as described herein, the non-naturally occurring microbial organisms and methods of the invention also can be utilized in various combinations with each other and/or with other microbial organisms and methods well known in the art to achieve product biosynthesis by other routes. For example, one alternative to produce butadiene or 2,4-pentadienoate other than use of the butadiene or 2,4-pentadienoate producers is through addition of another microbial organism capable of converting a butadiene or 2,4-pentadienoate pathway intermediate to butadiene or 2,4-pentadienoate. One such procedure includes, for example, the fermentation of a microbial organism that produces a butadiene or 2,4-pentadienoate pathway intermediate. The butadiene or 2,4-pentadienoate pathway intermediate can then be used as a substrate for a second microbial organism that converts the butadiene or 2,4-pentadienoate pathway intermediate to butadiene or 2,4-pentadienoate. The butadiene or 2,4-pentadienoate pathway intermediate can be added directly to another culture of the second organism or the original culture of the butadiene or 2,4-pentadienoate pathway intermediate producers can be depleted of these microbial organisms by, for example, cell separation, and then subsequent addition of the second organism to the fermentation broth can be utilized to produce the final product without intermediate purification steps.

In other embodiments, the non-naturally occurring microbial organisms and methods of the invention can be assembled in a wide variety of subpathways to achieve biosynthesis of, for example, butadiene or 2,4-pentadienoate. In these embodiments, biosynthetic pathways for a desired product of the invention can be segregated into different microbial organisms, and the different microbial organisms can be co-cultured to produce the final product. In such a biosynthetic scheme, the product of one microbial organism is the substrate for a second microbial organism until the final product is synthesized. For example, the biosynthesis of butadiene or 2,4-pentadienoate can be accomplished by constructing a microbial organism that contains biosynthetic pathways for conversion of one pathway intermediate to another pathway intermediate or the product. Alternatively, butadiene or 2,4-pentadienoate also can be biosynthetically produced from microbial organisms through co-culture or co-fermentation using two organisms in the same vessel, where the first microbial organism produces a butadiene or 2,4-pentadienoate intermediate and the second microbial organism converts the intermediate to butadiene or 2,4-pentadienoate.

Given the teachings and guidance provided herein, those skilled in the art will understand that a wide variety of combinations and permutations exist for the non-naturally occurring microbial organisms and methods of the invention together with other microbial organisms, with the co-culture of other non-naturally occurring microbial organisms having subpathways and with combinations of other chemical and/or biochemical procedures well known in the art to produce butadiene or 2,4-pentadienoate.

Similarly, it is understood by those skilled in the art that a host organism can be selected based on desired characteristics for introduction of one or more gene disruptions to increase production of butadiene or 2,4-pentadienoate. Thus, it is understood that, if a genetic modification is to be introduced into a host organism to disrupt a gene, any homologs, orthologs or paralogs that catalyze similar, yet non-identical metabolic reactions can similarly be disrupted to ensure that a desired metabolic reaction is sufficiently disrupted. Because certain differences exist among metabolic networks between different organisms, those skilled in the art will understand that the actual genes disrupted in a given organism may differ between organisms. However, given the teachings and guidance provided herein, those skilled in the art also will understand that the methods of the invention can be applied to any suitable host microorganism to identify the cognate metabolic alterations needed to construct an organism in a species of interest that will increase butadiene or 2,4-pentadienoate biosynthesis. In a particular embodiment, the increased production couples biosynthesis of butadiene or 2,4-pentadienoate to growth of the organism, and can obligatorily couple production of butadiene or 2,4-pentadienoate to growth of the organism if desired and as disclosed herein.

Sources of encoding nucleic acids for a butadiene or 2,4-pentadienoate pathway enzyme or protein can include, for example, any species where the encoded gene product is capable of catalyzing the referenced reaction. Such species include both prokaryotic and eukayotic organisms including, but not limited to, bacteria, including archaea and eubacteria, and eukaryotes, including yeast, plant, insect, animal, and mammal, including human. Exemplary species for such sources include, for example, Escherichia coli, Acidaminococcus fermentans, Acinetobacter baumannii Naval-82, Acinetobacter baylyi, Acinetobacter calcoaceticus, Acinetobacter sp. Strain M-1, Actinobacillus succinogenes 130Z Allochromatium vinosum DSM180, Aminomonas aminovorus, Anaerotruncus colihominis, Aquifex aeolicus VF5, Arabidopsis thaliana, Archaeglubus fulgidus, Archaeoglobus fulgidus DSM4304, Aspergillus niger, Aspergillus oryzae, Aspergillus terreus, Azotobacter vinelandii DJ, Bacillus alcalophilus ATCC 27647, Bacillus azotoformans LMG 9581, Bacillus cereus, Bacillus coagulans 36D1, Bacillus megaterium, Bacillus methanolicus MGA3, Bacillus methanolicus PB1, Bacillus pumilus, Bacillus selenitireducens MLS10, Bacillus smithii, Bacillus sphaericus, Bacillus subtilis, Bacteroides capillosus, Bifdobacterium animalis lactis, Bifdobacterium breve, Bifdobacterium dentium ATCC 27678, Bifdobacterium pseudolongum subsp. Globosum, Bos taurus, Burkholderia ambifaria AMMD, Burkholderia phymatum, Burkholderia stabilis, Burkholderia thailandensis E264, Burkholderia xenovorans, Burkholderia xenovorans LB400, butyrate-producing bacterium L2-50, Campylobacter curvus 525.92, Campylobacter jejuni, Candida albicans, Candida boidinii, Candida methylica, Candida tropicalis, Carboxydothermus hydrogenoformans, Carboxydothermus hydrogenoformans Z-2901, Caulobacter sp. AP7, Chlamydomonas reinhardtii, Chloroflexus aurantiacus, Chlorobiumphaeobacteroides DSM266, Chlorolexus aurantiacus J-10-fl, Chlorofexus aggregans DSM9485, Citrobacter koseri ATCC BAA-895, Clostridium acetobutylicum, Clostridium acetobutylicum ATCC 824, Clostridium acidurici, Clostridium aminobutyricum, Clostridium beijerinckii, Clostridium beijerinckii NRRL B593, Clostridium carboxidivorans P7, Clostridium cellulolyticum H10, Clostridium difficile, Clostridium kluyveri, Clostridium kluyveri DSM555, Clostridium ljungdahli, Clostridium jungdahlii DSM13528, Clostridium pasteurianum, Clostridium pasteurianum DSM525, Clostridium perfringens, Clostridium perfringens ATCC 13124, Clostridium perfringens str. 13, Clostridium propionicum, Clostridium saccharoperbutylacetonicum, Clostridium sporogens, Clostridum symbiosum, Clostridium tetani, Comamonas sp. CNB-1, Corynebacterium sp. U-96, Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032, Corynebacterium glutamicum R, Corynebacterium glutamicum ATCC 14067, Corynebacterium variabile, Cupriavidus necator, Cupriavidus necatorN-1, Cupriavidus taiwanensis, Cyanobium PCC7001, Deinococcus radiodurans RI, Desulfovibrio africanus str. Walvis Bay, Desulfovibrio fructosovorans JJ, Desulfatibacillum alkenivorans AK-01, Desulfotobacterium hafniense, Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774, Desulfotobacterium metallireducens DSM15288, Desulfotomaculum reducens MI-1, Dictyostelium discoideum AX4, Elizabethkingia meningoseptica, Erythrobacter sp. NAP1, Escherichia coli C, Escherichia coli K12, Escherichia coli K-12MG655, Escherichia coli W, Eubacterium barkeri, Flavobacterium figoris, Fusobacterium nucleatum, Geobacter bemidjiensis Bem, Geobacter metallireducens GS-5, Geobacillus sp. GHH01, Geobacillus sp. M10EXG, Geobacillus sp. Y4.1MC1, Geobacillus stearothermophilus, Geobacillus thermoglucosidasius, Geobacillus themodenitrifcans NG80-2, Geobacillus sp. Y4.1MC1, Geobacter sulfurreducens, Geobacter sulfurreducens PCA, Gibberella zeae, Haemophilus influenza, Haloarcula marismortui, Haloarcula marismortui ATCC 43049, Haloferax mediterranei ATCC 33500, Helicobacter pylori, Homo sapiens, Human gut metagenome, Hydrogenobacter thermophilus, Hydrogenobacter thermophilus TK-6, Hyphomicrobium denitrifcans ATCC 51888, Hyphomicrobium zavarzinii, Kineococcus radiotolerans, Klebsiella oxytoca, Klebsiella pneumonia, Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Kluyveromyces lactis, Lactobacillus acidophilus, Lactobacillus brevis ATCC 367, Lactobacillus paraplantarum, Lactobacillus plantarum, Lactobacillus reuteri, Lactobacillus sp. 30a, Leuconostoc mesenteroides, Lysinibacillus fusiformis, Marine metagenome JCVI SCAF 1096627185304, Marinobacter aquaeolei, Marine gamma proteobacterium HTCC2080, Mesorhizobium loti MAFF303099, Methanosarcina acetivorans C2A, Metallosphaera sedula, Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, Methanosarcina mazei Tuc01, Methylomonas aminofaciens, Methylobacterium extorquens, Methylobacterium extorquens AM1, Methylobacillus flagellates, Methylobacillus flagellatus KT, Methylovorus glucosetrophus SIP3-4, Methylobacter marinus, Methylococcus capsulatis, Methylomicrobium album BG8, Microlunatus phosphovorus NM-1, Methylovorus sp. MP688, Methylovorus glucosetrophus SIP3-4, Moorella thermoacetica, Mus musculus, Mycobacterium avium, Mycobacterium avium subsp., Mycobacterium avium subsp. paratuberculosis K-10, Mycobacterium bovis BCG, Mycobacterium gastri, Mycobacterium marinum M, Mycobacterium smegmatis, Mycobacterium smegmatis MC2 155, Mycobacter sp. strain JC1 DSM 3803, Mycobacterium tuberculosis, Natranaerobius thermophilus, Neosartorya fzscheri, Nicotiana glutinosa, Nitrososphaera gargensis Ga9.2, Nocardia farcinica IFM10152, Nocardia iowensis (sp. NRRL 5646), Nostoc sp. PCC 7120, Ogataea parapolymorpha DL-1 (Hansenula polymorpha DL-1), Oryctolagus cuniculus, Oxalobacter formigenes, Paenibacillus peoriae KCTC 3763, Paracoccus denitrificans, Pedicoccus pentosaceus, Pelobacter carbinolicus DSM2380, Pelotomaculum thermopropionicum, Penicillium chrysogenum, Photobacterium phosphoreum, Photobacterium profundum 3TCK Pichia pastoris, Pichia stipitis, Picrophilus torridus DSM9790, Porphyromonas gingivalis, Porphyromonas gingivalis W83, Pratuberculosis, Propionibacterium acidipropionici ATCC 4875, Propionibacterium acnes KPAI71202, Pseudomonas aeruginosa, Pseudomonas aeruginosa PA01, Pseudomonas aeruginosa PAO1, Pseudomonas fluorescens, Pseudomonas fluorescens KU-7, Pseudomonas knackmussii (B13), Pseudomonas mendocina, Pseudomonas putida, Pseudomonas putida KT2440, Pseudomonas sp, Pseudomonas sp. CF600, Pseudomonas syringae pv. syringae B728a, Psychroflexus torquis ATCC 700755, Pyrobaculum aerophilum str. M2, Pyrococcus abyssi, Pyrococcus furiosus, Pyrococcus horikoshii OT3, Pyrobaculum islandicum DSM 4184, Ralstonia eutropha, Ralstonia eutropha H16, Ralstonia eutropha JMP134, Ralstonia metallidurans, Ralstonia pickettii, Rattus norvegicus, Rhizobium leguminosarum, Rhodobacter capsulatus, Rhodobacter sphaeroides, Rhodobacter sphaeroides ATCC 17025, Rhodococcus ruber, Rhodopseudomonas palustris, Rhodopseudomonas palustris CGA009, Rhodospirillum rubrum, Roseiflexus castenholzii, Saccharomyces cerevisae, Saccharomyces cerevisiae S288c, Salinispora arenicola, Salmonella enterica, Salmonella typhimurium, Salmonella typhimurium LT2, Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, Schizosaccharomyces pombe, Selenomonas ruminantium, Shewanella oneidensis MR-1, Simmondsia chinensis, Sinorhizobium meliloti 1021, Streptomyces griseus subsp. griseus NBRC 13350, Streptococcus pyogenes ATCC 10782, Sulfolobus acidocalarius, Sulfolobus solfataricus, Sulfolobus solfataricus P-2, Sulfolobus tokodaii, Synechocystis str. PCC 6803, Syntrophobacter fumaroxidans, Syntrophus aciditrophicus, Thauera aromatic, Thermoanaerobacter brockii HTD4, Thermoanaerobacter sp. X514, Thermoanaerobacter tengcongensis MB4, Thermococcus kodakaraensis, Thermococcus litoralis, Thermoplasma acidophilum, Thermoproteus neutrophilus, Thermotoga maritima, Thermus thermophilus, Thiocapsa roseopersicina Trichomonas vaginalis G3, Trypanosoma brucei, Tsukamurella paurometabola DSM 20162, Vibrio cholera, Vibrio harveyi ATCC BAA-1116, Vibrio parahaemolyticus, Vibrio vulnificus, Xanthobacter autotrophicus Py2, Yarrowia lipolytica, Yersinia pestis, Zea mays, Zoogloea ramigera, Zymomonas mobilis, as well as other exemplary species disclosed herein or available as source organisms for corresponding genes. However, with the complete genome sequence available for now more than 550 species (with more than half of these available on public databases such as the NCBI), including 395 microorganism genomes and a variety of yeast, fungi, plant, and mammalian genomes, the identification of genes encoding the requisite butadiene or 2,4-pentadienoate biosynthetic activity for one or more genes in related or distant species, including for example, homologues, orthologs, paralogs and nonorthologous gene displacements of known genes, and the interchange of genetic alterations between organisms is routine and well known in the art. Accordingly, the metabolic alterations allowing biosynthesis of butadiene or 2,4-pentadienoate described herein with reference to a particular organism such as E. coli can be readily applied to other microorganisms, including prokaryotic and eukaryotic organisms alike. Given the teachings and guidance provided herein, those skilled in the art will know that a metabolic alteration exemplified in one organism can be applied equally to other organisms.

In some instances, such as when an alternative butadiene or 2,4-pentadienoate biosynthetic pathway exists in an unrelated species, butadiene or 2,4-pentadienoate biosynthesis can be conferred onto the host species by, for example, exogenous expression of a paralog or paralogs from the unrelated species that catalyzes a similar, yet non-identical metabolic reaction to replace the referenced reaction. Because certain differences among metabolic networks exist between different organisms, those skilled in the art will understand that the actual gene usage between different organisms may differ. However, given the teachings and guidance provided herein, those skilled in the art also will understand that the teachings and methods of the invention can be applied to all microbial organisms using the cognate metabolic alterations to those exemplified herein to construct a microbial organism in a species of interest that will synthesize butadiene or 2,4-pentadienoate.

A nucleic acid molecule encoding a butadiene or 2,4-pentadienoate pathway enzyme or protein of the invention can also include a nucleic acid molecule that hybridizes to a nucleic acid disclosed herein by SEQ ID NO, GenBank and/or GI number or a nucleic acid molecule that hybridizes to a nucleic acid molecule that encodes an amino acid sequence disclosed herein by SEQ ID NO, GenBank and/or GI number. Hybridization conditions can include highly stringent, moderately stringent, or low stringency hybridization conditions that are well known to one of skill in the art such as those described herein. Similarly, a nucleic acid molecule that can be used in the invention can be described as having a certain percent sequence identity to a nucleic acid disclosed herein by SEQ ID NO, GenBank and/or GI number or a nucleic acid molecule that hybridizes to a nucleic acid molecule that encodes an amino acid sequence disclosed herein by SEQ ID NO, GenBank and/or GI number. For example, the nucleic acid molecule can have at least 65%, 70%, 75%, 80% 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity, or be identical, to a nucleic acid described herein.

Stringent hybridization refers to conditions under which hybridized polynucleotides are stable. As known to those of skill in the art, the stability of hybridized polynucleotides is reflected in the melting temperature (T_(m)) of the hybrids. In general, the stability of hybridized polynucleotides is a function of the salt concentration, for example, the sodium ion concentration and temperature. A hybridization reaction can be performed under conditions of lower stringency, followed by washes of varying, but higher, stringency. Reference to hybridization stringency relates to such washing conditions. Highly stringent hybridization includes conditions that permit hybridization of only those nucleic acid sequences that form stable hybridized polynucleotides in 0.018M NaCl at 65° C., for example, if a hybrid is not stable in 0.018M NaCl at 65° C., it will not be stable under high stringency conditions, as contemplated herein. High stringency conditions can be provided, for example, by hybridization in 50% formamide, 5× Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.1×SSPE, and 0.1% SDS at 65° C. Hybridization conditions other than highly stringent hybridization conditions can also be used to describe the nucleic acid sequences disclosed herein. For example, the phrase moderately stringent hybridization refers to conditions equivalent to hybridization in 50% formamide, 5× Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.2×SSPE, 0.2% SDS, at 42° C. The phrase low stringency hybridization refers to conditions equivalent to hybridization in 10% formamide, 5× Denhart's solution, 6×SSPE, 0.2% SDS at 22° C., followed by washing in 1×SSPE, 0.2% SDS, at 37° C. Denhart's solution contains 1% Ficoll, 1% polyvinylpyrolidone, and 1% bovine serum albumin (BSA). 20×SSPE (sodium chloride, sodium phosphate, ethylene diamide tetraacetic acid (EDTA)) contains 3M sodium chloride, 0.2M sodium phosphate, and 0.025 M (EDTA). Other suitable low, moderate and high stringency hybridization buffers and conditions are well known to those of skill in the art and are described, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Ed., Cold Spring Harbor Laboratory, New York (2001); and Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999).

A nucleic acid molecule encoding a butadiene or 2,4-pentadienoate pathway enzyme or protein of the invention can have at least a certain sequence identity to a nucleotide sequence disclosed herein. According, in some aspects of the invention, a nucleic acid molecule encoding a butadiene or 2,4-pentadienoate pathway enzyme or protein has a nucleotide sequence of at least 65% identity, at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 91% identity, at least 92% identity, at least 93% identity, at least 94% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity, or is identical, to a nucleic acid disclosed herein by SEQ ID NO, GenBank and/or GI number or a nucleic acid molecule that hybridizes to a nucleic acid molecule that encodes an amino acid sequence disclosed herein by SEQ ID NO, GenBank and/or GI number.

Sequence identity (also known as homology or similarity) refers to sequence similarity between two nucleic acid molecules or between two polypeptides. Identity can be determined by comparing a position in each sequence, which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are identical at that position. A degree of identity between sequences is a function of the number of matching or homologous positions shared by the sequences. The alignment of two sequences to determine their percent sequence identity can be done using software programs known in the art, such as, for example, those described in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999). Preferably, default parameters are used for the alignment. One alignment program well known in the art that can be used is BLAST set to default parameters. In particular, programs are BLASTN and BLASTP, using the following default parameters: Genetic code=standard; filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+SwissProtein+SPupdate+PIR. Details of these programs can be found at the National Center for Biotechnology Information.

Methods for constructing and testing the expression levels of a non-naturally occurring butadiene or 2,4-pentadienoate—producing host can be performed, for example, by recombinant and detection methods well known in the art. Such methods can be found described in, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Ed., Cold Spring Harbor Laboratory, New York (2001); and Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999).

Exogenous nucleic acid sequences involved in a pathway for production of butadiene or 2,4-pentadienoate can be introduced stably or transiently into a host cell using techniques well known in the art including, but not limited to, conjugation, electroporation, chemical transformation, transduction, transfection, and ultrasound transformation. For exogenous expression in E. coli or other prokaryotic cells, some nucleic acid sequences in the genes or cDNAs of eukaryotic nucleic acids can encode targeting signals such as an N-terminal mitochondrial or other targeting signal, which can be removed before transformation into prokaryotic host cells, if desired. For example, removal of a mitochondrial leader sequence led to increased expression in E. coli (Hoffmeister et al., J. Biol. Chem. 280:4329-4338 (2005)). For exogenous expression in yeast or other eukaryotic cells, genes can be expressed in the cytosol without the addition of leader sequence, or can be targeted to mitochondrion or other organelles, or targeted for secretion, by the addition of a suitable targeting sequence such as a mitochondrial targeting or secretion signal suitable for the host cells. Thus, it is understood that appropriate modifications to a nucleic acid sequence to remove or include a targeting sequence can be incorporated into an exogenous nucleic acid sequence to impart desirable properties. Furthermore, genes can be subjected to codon optimization with techniques well known in the art to achieve optimized expression of the proteins.

An expression vector or vectors can be constructed to include one or more butadiene or 2,4-pentadienoate biosynthetic pathway encoding nucleic acids as exemplified herein operably linked to expression control sequences functional in the host organism. Expression vectors applicable for use in the microbial host organisms of the invention include, for example, plasmids, phage vectors, viral vectors, episomes and artificial chromosomes, including vectors and selection sequences or markers operable for stable integration into a host chromosome. Additionally, the expression vectors can include one or more selectable marker genes and appropriate expression control sequences. Selectable marker genes also can be included that, for example, provide resistance to antibiotics or toxins, complement auxotrophic deficiencies, or supply critical nutrients not in the culture media. Expression control sequences can include constitutive and inducible promoters, transcription enhancers, transcription terminators, and the like which are well known in the art. When two or more exogenous encoding nucleic acids are to be co-expressed, both nucleic acids can be inserted, for example, into a single expression vector or in separate expression vectors. For single vector expression, the encoding nucleic acids can be operationally linked to one common expression control sequence or linked to different expression control sequences, such as one inducible promoter and one constitutive promoter. The transformation of exogenous nucleic acid sequences involved in a metabolic or synthetic pathway can be confirmed using methods well known in the art. Such methods include, for example, nucleic acid analysis such as Northern blots or polymerase chain reaction (PCR) amplification of mRNA, or immunoblotting for expression of gene products, or other suitable analytical methods to test the expression of an introduced nucleic acid sequence or its corresponding gene product. It is understood by those skilled in the art that the exogenous nucleic acid is expressed in a sufficient amount to produce the desired product, and it is further understood that expression levels can be optimized to obtain sufficient expression using methods well known in the art and as disclosed herein.

In some embodiments, the present invention provides a method for producing butadiene including culturing a non-naturally occurring microbial organism disclosed herein under conditions and for a sufficient period of time to produce butadiene. In some aspects, the method further includes separating the butadiene from other components in the culture.

In some embodiments, the present invention provides a method for producing butadiene and hydrogen including culturing a non-naturally occurring microbial organism disclosed herein under conditions and for a sufficient period of time to produce butadiene and hydrogen. In some aspects, the method further includes separating the butadiene and hydrogen from other components in the culture. In some aspects, the hydrogen is separated by shaking.

In some embodiments, the present invention provides a method for producing 2,4-pentadienoate including culturing a non-naturally occurring microbial organism disclosed herein under conditions and for a sufficient period of time to produce 2,4-pentadienoate. In some aspects, the method further includes separating the 2,4-pentadienoate from other components in the culture.

In some embodiments, the present invention provides a method for producing 2,4-pentadienoate and hydrogen including culturing a non-naturally occurring microbial organism disclosed herein under conditions and for a sufficient period of time to produce 2,4-pentadienoate and hydrogen. In some aspects, the method further includes separating the 2,4-pentadienoate and hydrogen from other components in the culture. In some aspects, the hydrogen is separated by shaking.

Suitable purification and/or assays to test for the production of butadiene or 2,4-pentadienoate can be performed using well known methods. Suitable replicates such as triplicate cultures can be grown for each engineered strain to be tested. For example, product and byproduct formation in the engineered production host can be monitored. The final product and intermediates, and other organic compounds, can be analyzed by methods such as HPLC (High Performance Liquid Chromatography), GC-MS (Gas Chromatography-Mass Spectroscopy) and LC-MS (Liquid Chromatography-Mass Spectroscopy) or other suitable analytical methods using routine procedures well known in the art. The release of product in the fermentation broth can also be tested with the culture supernatant. Byproducts and residual glucose can be quantified by HPLC using, for example, a refractive index detector for glucose and alcohols, and a UV detector for organic acids (Lin et al., Biotechnol. Bioeng. 90:775-779 (2005)), or other suitable assay and detection methods well known in the art. The individual enzyme or protein activities from the exogenous DNA sequences can also be assayed using methods well known in the art. As described herein, Headspace GCMS analysis can be carried out on a 7890A GC with 5975C inert MSD using a GS-GASPRO column, 30m×0.32 mm (Agilent Technologies). Static headspace sample introduction can be performed on a CombiPAL autosampler (CTC Analytics) following 2 min incubation at 45° C.

The butadiene or 2,4-pentadienoate can be separated from other components in the culture using a variety of methods well known in the art. Such separation methods include, for example, extraction procedures as well as methods that include continuous liquid-liquid extraction, pervaporation, membrane filtration, membrane separation, reverse osmosis, electrodialysis, distillation, crystallization, centrifugation, extractive filtration, ion exchange chromatography, size exclusion chromatography, adsorption chromatography, and ultrafiltration. All of the above methods are well known in the art. Additionally, because butadiene can be a gas at fermentation temperatures, it can also be separated and capture accordingly. Exemplary methods to separate and capture gaseous butadiene are described herein.

Any of the non-naturally occurring microbial organisms described herein can be cultured to produce and/or secrete the biosynthetic products of the invention. For example, the butadiene or 2,4-pentadienoate producers can be cultured for the biosynthetic production of butadiene or 2,4-pentadienoate. Accordingly, in some embodiments, the invention provides culture medium containing the butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate described herein. In some aspects, the culture medium can also be separated from the non-naturally occurring microbial organisms of the invention that produced the butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate. Methods for separating a microbial organism from culture medium are well known in the art. Exemplary methods include filtration, flocculation, precipitation, centrifugation, sedimentation, and the like.

For the production of butadiene or 2,4-pentadienoate, the recombinant strains are cultured in a medium with carbon source and other essential nutrients. It is sometimes desirable and can be highly desirable to maintain anaerobic conditions in the fermenter to reduce the cost of the overall process. Such conditions can be obtained, for example, by first sparging the medium with nitrogen and then sealing the flasks with a septum and crimp-cap. For strains where growth is not observed anaerobically, microaerobic or substantially anaerobic conditions can be applied by perforating the septum with a small hole for limited aeration. Exemplary anaerobic conditions have been described previously and are well-known in the art. Exemplary aerobic and anaerobic conditions are described, for example, in United State publication 2009/0047719, filed Aug. 10, 2007. Fermentations can be performed in a batch, fed-batch or continuous manner, as disclosed herein. Fermentations can also be conducted in two phases, if desired. The first phase can be aerobic to allow for high growth and therefore high productivity, followed by an anaerobic phase of high butadiene or 2,4-pentadienoate yields.

If desired, the pH of the medium can be maintained at a desired pH, in particular neutral pH, such as a pH of around 7 by addition of a base, such as NaOH or other bases, or acid, as needed to maintain the culture medium at a desirable pH. The growth rate can be determined by measuring optical density using a spectrophotometer (600 nm), and the glucose uptake rate by monitoring carbon source depletion over time.

The growth medium can include, for example, any carbohydrate source which can supply a source of carbon to the non-naturally occurring microorganism. Such sources include, for example: sugars such as glucose, xylose, arabinose, galactose, mannose, fructose, sucrose, starch, methanol, syngas, or glycerol, and it is understood that a carbon source can be used alone as the sole source of carbon or in combination with other carbon sources described herein or known in the art. Other sources of carbohydrate include, for example, renewable feedstocks and biomass. Exemplary types of biomasses that can be used as feedstocks in the methods of the invention include cellulosic biomass, hemicellulosic biomass and lignin feedstocks or portions of feedstocks. Such biomass feedstocks contain, for example, carbohydrate substrates useful as carbon sources such as glucose, xylose, arabinose, galactose, mannose, fructose and starch. Given the teachings and guidance provided herein, those skilled in the art will understand that renewable feedstocks and biomass other than those exemplified above also can be used for culturing the microbial organisms of the invention for the production of butadiene or 2,4-pentadienoate.

In addition to the feedstocks, including the renewable feedstocks such as those exemplified above, the butadiene or 2,4-pentadienoate microbial organisms of the invention also can be modified for growth on syngas as its source of carbon or on methane. In this specific embodiment, one or more proteins or enzymes are expressed in the butadiene or 2,4-pentadienoate producing organisms to provide a metabolic pathway for utilization of syngas, methane or other gaseous carbon source. In the case of methane the organism can be a natural methanotroph including those mentioned herein, or a non-methanotroph such as E. coli that is genetically engineered to use methane such as by expression of methane monooxygenase (MMO), the methanol produced can be utilized as described herein.

Synthesis gas, also known as syngas or producer gas, is the major product of gasification of coal and of carbonaceous materials such as biomass materials, including agricultural crops and residues. Syngas is a mixture primarily of H₂ and CO and can be obtained from the gasification of any organic feedstock, including but not limited to coal, coal oil, natural gas, biomass, and waste organic matter. Gasification is generally carried out under a high fuel to oxygen ratio. Although largely H₂ and CO, syngas can also include CO₂ and other gases in smaller quantities. Thus, synthesis gas provides a cost effective source of gaseous carbon such as CO and, additionally, CO₂.

The Wood-Ljungdahl pathway catalyzes the conversion of CO and H₂ to acetyl-CoA and other products such as acetate. Organisms capable of utilizing CO and syngas also generally have the capability of utilizing CO₂ and CO₂/H₂ mixtures through the same basic set of enzymes and transformations encompassed by the Wood-Ljungdahl pathway. H₂-dependent conversion of CO₂ to acetate by microorganisms was recognized long before it was revealed that CO also could be used by the same organisms and that the same pathways were involved. Many acetogens have been shown to grow in the presence of CO₂ and produce compounds such as acetate as long as hydrogen is present to supply the necessary reducing equivalents (see for example, Drake, Acetogenesis, pp. 3-60 Chapman and Hall, New York, (1994)). This can be summarized by the following equation: 2CO₂+4H₂ +nADP+nPi→CH₃COOH+2H₂O+nATP

Hence, non-naturally occurring microorganisms possessing the Wood-Ljungdahl pathway can utilize CO₂ and H₂ mixtures as well for the production of acetyl-CoA and other desired products.

The Wood-Ljungdahl pathway is well known in the art and consists of 12 reactions which can be separated into two branches: (1) methyl branch and (2) carbonyl branch. The methyl branch converts syngas to methyltetrahydrofolate (methyl-THF) whereas the carbonyl branch converts methyl-THF to acetyl-CoA. The reactions in the methyl branch are catalyzed in order by the following enzymes or proteins: ferredoxin oxidoreductase, formate dehydrogenase, formyltetrahydrofolate synthetase, methenyltetrahydrofolate cyclodehydratase, methylenetetrahydrofolate dehydrogenase and methylenetetrahydrofolate reductase. The reactions in the carbonyl branch are catalyzed in order by the following enzymes or proteins: methyltetrahydrofolate:corrinoid protein methyltransferase (for example, AcsE), corrinoid iron-sulfur protein, nickel-protein assembly protein (for example, AcsF), ferredoxin, acetyl-CoA synthase, carbon monoxide dehydrogenase and nickel-protein assembly protein (for example, CooC). Following the teachings and guidance provided herein for introducing a sufficient number of encoding nucleic acids to generate a butadiene or 2,4-pentadienoate pathway, those skilled in the art will understand that the same engineering design also can be performed with respect to introducing at least the nucleic acids encoding the Wood-Ljungdahl enzymes or proteins absent in the host organism. Therefore, introduction of one or more encoding nucleic acids into the microbial organisms of the invention such that the modified organism contains the complete Wood-Ljungdahl pathway will confer syngas utilization ability.

Additionally, the reductive (reverse) tricarboxylic acid cycle coupled with carbon monoxide dehydrogenase and/or hydrogenase activities can also be used for the conversion of CO, CO₂ and/or H₂ to acetyl-CoA and other products such as acetate. Organisms capable of fixing carbon via the reductive TCA pathway can utilize one or more of the following enzymes: ATP citrate-lyase, citrate lyase, aconitase, isocitrate dehydrogenase, alpha-ketoglutamte:ferredoxin oxidoreductase, succinyl-CoA synthetase, succinyl-CoA transferase, fumarate reductase, fumarase, malate dehydrogenase, NAD(P)H:ferredoxin oxidoreductase, carbon monoxide dehydrogenase, and hydrogenase. Specifically, the reducing equivalents extracted from CO and/or H₂ by carbon monoxide dehydrogenase and hydrogenase are utilized to fix CO₂ via the reductive TCA cycle into acetyl-CoA or acetate. Acetate can be converted to acetyl-CoA by enzymes such as acetyl-CoA transferase, acetate kinase/phosphotransacetylase, and acetyl-CoA synthetase. Acetyl-CoA can be converted to the butadiene or 2,4-pentadienoate precursors, glyceraldehyde-3-phosphate, phosphoenolpyruvate, and pyruvate, by pyruvate:ferredoxin oxidoreductase and the enzymes of gluconeogenesis. Following the teachings and guidance provided herein for introducing a sufficient number of encoding nucleic acids to generate a butadiene or 2,4-pentadienoate pathway, those skilled in the art will understand that the same engineering design also can be performed with respect to introducing at least the nucleic acids encoding the reductive TCA pathway enzymes or proteins absent in the host organism. Therefore, introduction of one or more encoding nucleic acids into the microbial organisms of the invention such that the modified organism contains a reductive TCA pathway can confer syngas utilization ability.

Accordingly, given the teachings and guidance provided herein, those skilled in the art will understand that a non-naturally occurring microbial organism can be produced that secretes the biosynthesized compounds of the invention when grown on a carbon source such as a carbohydrate. Such compounds include, for example, butadiene or 2,4-pentadienoate and any of the intermediate metabolites in the butadiene or 2,4-pentadienoate pathway. All that is required is to engineer in one or more of the required enzyme or protein activities to achieve biosynthesis of the desired compound or intermediate including, for example, inclusion of some or all of the butadiene or 2,4-pentadienoate biosynthetic pathways. Accordingly, the invention provides a non-naturally occurring microbial organism that produces and/or secretes butadiene or 2,4-pentadienoate when grown on a carbohydrate or other carbon source and produces and/or secretes any of the intermediate metabolites shown in the butadiene or 2,4-pentadienoate pathway when grown on a carbohydrate or other carbon source. The butadiene or 2,4-pentadienoate producing microbial organisms of the invention can initiate synthesis from an intermediate, for example, 4-hydroxy-2-oxovalerate, 2-oxopentenoate, 2-oxopentenoyl-CoA, 2-hydroxypentenoyl-CoA, 2,4-Pentadienoyl-CoA, 2-hydroxypentenoate, malonyl-CoA, 3-Oxoglutaryl-CoA, 3-hydroxyglutaryl-CoA, 3-hydroxyglutaryl-phosphate, 3-hydroxy-5-oxopentanoate, 3,5-dihydroxypentanoate, 3,5-dihydroxypentanoyl-CoA, 5-hydroxypent-2-enoyl-CoA, 2,4-pentadienoyl-CoA, 3,5-dihydroxypentanoate, or 5-hydroxypent-2-enoate.

The non-naturally occurring microbial organisms of the invention are constructed using methods well known in the art as exemplified herein to exogenously express at least one nucleic acid encoding a butadiene or 2,4-pentadienoate pathway enzyme or protein in sufficient amounts to produce butadiene or 2,4-pentadienoate. It is understood that the microbial organisms of the invention are cultured under conditions sufficient to produce butadiene or 2,4-pentadienoate. Following the teachings and guidance provided herein, the non-naturally occurring microbial organisms of the invention can achieve biosynthesis of butadiene or 2,4-pentadienoate resulting in intracellular concentrations between about 0.01-200 mM or more. Generally, the intracellular concentration of butadiene or 2,4-pentadienoate is between about 3-150 mM, particularly between about 5-125 mM and more particularly between about 8-100 mM, including about 10 mM, 20 mM, 50 mM, 80 mM, or more. Intracellular concentrations between and above each of these exemplary ranges also can be achieved from the non-naturally occurring microbial organisms of the invention.

In some embodiments, culture conditions include anaerobic or substantially anaerobic growth or maintenance conditions. Exemplary anaerobic conditions have been described previously and are well known in the art. Exemplary anaerobic conditions for fermentation processes are described herein and are described, for example, in U.S. publication 2009/0047719, filed Aug. 10, 2007. Any of these conditions can be employed with the non-naturally occurring microbial organisms as well as other anaerobic conditions well known in the art. Under such anaerobic or substantially anaerobic conditions, the butadiene or 2,4-pentadienoate producers can synthesize butadiene or 2,4-pentadienoate at intracellular concentrations of 5-10 mM or more as well as all other concentrations exemplified herein. It is understood that, even though the above description refers to intracellular concentrations, butadiene or 2,4-pentadienoate producing microbial organisms can produce butadiene or 2,4-pentadienoate intracellularly and/or secrete the product into the culture medium.

Exemplary fermentation processes include, but are not limited to, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation; and continuous fermentation and continuous separation. In an exemplary batch fermentation protocol, the production organism is grown in a suitably sized bioreactor sparged with an appropriate gas. Under anaerobic conditions, the culture is sparged with an inert gas or combination of gases, for example, nitrogen, N₂/CO₂ mixture, argon, helium, and the like. As the cells grow and utilize the carbon source, additional carbon source(s) and/or other nutrients are fed into the bioreactor at a rate approximately balancing consumption of the carbon source and/or nutrients. The temperature of the bioreactor is maintained at a desired temperature, generally in the range of 22-37 degrees C., but the temperature can be maintained at a higher or lower temperature depending on the growth characteristics of the production organism and/or desired conditions for the fermentation process. Growth continues for a desired period of time to achieve desired characteristics of the culture in the fermenter, for example, cell density, product concentration, and the like. In a batch fermentation process, the time period for the fermentation is generally in the range of several hours to several days, for example, 8 to 24 hours, or 1, 2, 3, 4 or 5 days, or up to a week, depending on the desired culture conditions. The pH can be controlled or not, as desired, in which case a culture in which pH is not controlled will typically decrease to pH 3-6 by the end of the run. Upon completion of the cultivation period, the fermenter contents can be passed through a cell separation unit, for example, a centrifuge, filtration unit, and the like, to remove cells and cell debris. In the case where the desired product is expressed intracellularly, the cells can be lysed or disrupted enzymatically or chemically prior to or after separation of cells from the fermentation broth, as desired, in order to release additional product. The fermentation broth can be transferred to a product separations unit. Isolation of product occurs by standard separations procedures employed in the art to separate a desired product from dilute aqueous solutions. Such methods include, but are not limited to, liquid-liquid extraction using a water immiscible organic solvent (e.g., toluene or other suitable solvents, including but not limited to diethyl ether, ethyl acetate, tetrahydrofuran (THF), methylene chloride, chloroform, benzene, pentane, hexane, heptane, petroleum ether, methyl tertiary butyl ether (MTBE), dioxane, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), and the like) to provide an organic solution of the product, if appropriate, standard distillation methods, and the like, depending on the chemical characteristics of the product of the fermentation process.

In an exemplary fully continuous fermentation protocol, the production organism is generally first grown up in batch mode in order to achieve a desired cell density. When the carbon source and/or other nutrients are exhausted, feed medium of the same composition is supplied continuously at a desired rate, and fermentation liquid is withdrawn at the same rate. Under such conditions, the product concentration in the bioreactor generally remains constant, as well as the cell density. The temperature of the fermenter is maintained at a desired temperature, as discussed above. During the continuous fermentation phase, it is generally desirable to maintain a suitable pH range for optimized production. The pH can be monitored and maintained using routine methods, including the addition of suitable acids or bases to maintain a desired pH range. The bioreactor is operated continuously for extended periods of time, generally at least one week to several weeks and up to one month, or longer, as appropriate and desired. The fermentation liquid and/or culture is monitored periodically, including sampling up to every day, as desired, to assure consistency of product concentration and/or cell density. In continuous mode, fermenter contents are constantly removed as new feed medium is supplied. The exit stream, containing cells, medium, and product, are generally subjected to a continuous product separations procedure, with or without removing cells and cell debris, as desired. Continuous separations methods employed in the art can be used to separate the product from dilute aqueous solutions, including but not limited to continuous liquid-liquid extraction using a water immiscible organic solvent (e.g., toluene or other suitable solvents, including but not limited to diethyl ether, ethyl acetate, tetrahydrofuran (THF), methylene chloride, chloroform, benzene, pentane, hexane, heptane, petroleum ether, methyl tertiary butyl ether (MTBE), dioxane, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), and the like), standard continuous distillation methods, and the like, or other methods well known in the art.

In addition to the culturing and fermentation conditions disclosed herein, growth condition for achieving biosynthesis of butadiene or 2,4-pentadienoate can include the addition of an osmoprotectant to the culturing conditions. In certain embodiments, the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented as described herein in the presence of an osmoprotectant. Briefly, an osmoprotectant refers to a compound that acts as an osmolyte and helps a microbial organism as described herein survive osmotic stress. Osmoprotectants include, but are not limited to, betaines, amino acids, and the sugar trehalose. Non-limiting examples of such are glycine betaine, praline betaine, dimethylthetin, dimethylslfonioproprionate, 3-dimethylsulfonio-2-methylproprionate, pipecolic acid, dimethylsulfonioacetate, choline, L-camitine and ectoine. In one aspect, the osmoprotectant is glycine betaine. It is understood to one of ordinary skill in the art that the amount and type of osmoprotectant suitable for protecting a microbial organism described herein from osmotic stress will depend on the microbial organism used. The amount of osmoprotectant in the culturing conditions can be, for example, no more than about 0.1 mM, no more than about 0.5 mM, no more than about 1.0 mM, no more than about 1.5 mM, no more than about 2.0 mM, no more than about 2.5 mM, no more than about 3.0 mM, no more than about 5.0 mM, no more than about 7.0 mM, no more than about 10 mM, no more than about 50 mM, no more than about 100 mM or no more than about 500 mM.

In some embodiments, the carbon feedstock and other cellular uptake sources such as phosphate, ammonia, sulfate, chloride and other halogens can be chosen to alter the isotopic distribution of the atoms present in butadiene or 2,4-pentadienoate or any butadiene or 2,4-pentadienoate pathway intermediate. The various carbon feedstock and other uptake sources enumerated above will be referred to herein, collectively, as “uptake sources.” Uptake sources can provide isotopic enrichment for any atom present in the product butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate, or for side products generated in reactions diverging away from a butadiene or 2,4-pentadienoate pathway. Isotopic enrichment can be achieved for any target atom including, for example, carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, chloride or other halogens.

In some embodiments, the uptake sources can be selected to alter the carbon-12, carbon-13, and carbon-14 ratios. In some embodiments, the uptake sources can be selected to alter the oxygen-16, oxygen-17, and oxygen-18 ratios. In some embodiments, the uptake sources can be selected to alter the hydrogen, deuterium, and tritium ratios. In some embodiments, the uptake sources can be selected to alter the nitrogen-14 and nitrogen-15 ratios. In some embodiments, the uptake sources can be selected to alter the sulfur-32, sulfur-33, sulfur-34, and sulfur-35 ratios. In some embodiments, the uptake sources can be selected to alter the phosphorus-31, phosphorus-32, and phosphorus-33 ratios. In some embodiments, the uptake sources can be selected to alter the chlorine-35, chlorine-36, and chlorine-37 ratios.

In some embodiments, the isotopic ratio of a target atom can be varied to a desired ratio by selecting one or more uptake sources. An uptake source can be derived from a natural source, as found in nature, or from a man-made source, and one skilled in the art can select a natural source, a man-made source, or a combination thereof, to achieve a desired isotopic ratio of a target atom. An example of a man-made uptake source includes, for example, an uptake source that is at least partially derived from a chemical synthetic reaction. Such isotopically enriched uptake sources can be purchased commercially or prepared in the laboratory and/or optionally mixed with a natural source of the uptake source to achieve a desired isotopic ratio. In some embodiments, a target atom isotopic ratio of an uptake source can be achieved by selecting a desired origin of the uptake source as found in nature. For example, as discussed herein, a natural source can be a biobased derived from or synthesized by a biological organism or a source such as petroleum-based products or the atmosphere. In some such embodiments, a source of carbon, for example, can be selected from a fossil fuel-derived carbon source, which can be relatively depleted of carbon-14, or an environmental or atmospheric carbon source, such as CO₂, which can possess a larger amount of carbon-14 than its petroleum-derived counterpart.

The unstable carbon isotope carbon-14 or radiocarbon makes up for roughly 1 in 10¹² carbon atoms in the earth's atmosphere and has a half-life of about 5700 years. The stock of carbon is replenished in the upper atmosphere by a nuclear reaction involving cosmic rays and ordinary nitrogen (¹⁴N). Fossil fuels contain no carbon-14, as it decayed long ago. Burning of fossil fuels lowers the atmospheric carbon-14 function, the so-called “Suess effect”.

Methods of determining the isotopic ratios of atoms in a compound are well known to those skilled in the art. Isotopic enrichment is readily assessed by mass spectrometry using techniques known in the art such as accelerated mass spectrometry (AMS), Stable Isotope Ratio Mass Spectrometry (SIRMS) and Site-Specific Natural Isotopic Fractionation by Nuclear Magnetic Resonance (SNIF-NMR). Such mass spectral techniques can be integrated with separation techniques such as liquid chromatography (LC), high performance liquid chromatography (HPLC) and/or gas chromatography, and the like.

In the case of carbon, ASTM D6866 was developed in the United States as a standardized analytical method for determining the biobased content of solid, liquid, and gaseous samples using radiocarbon dating by the American Society for Testing and Materials (ASTM) International. The standard is based on the use of radiocarbon dating for the determination of a product's biobased content. ASTM D6866 was first published in 2004, and the current active version of the standard is ASTM D6866-11 (effective Apr. 1, 2011). Radiocarbon dating techniques are well known to those skilled in the art, including those described herein.

The biobased content of a compound is estimated by the ratio of carbon-14 (¹⁴C) to carbon-12 (¹²C). Specifically, the Fraction Modern (Fm) is computed from the expression: Fm=(S−B)/(M−B), where B, S and M represent the ¹⁴C/¹²C ratios of the blank, the sample and the modern reference, respectively. Fraction Modern is a measurement of the deviation of the ¹⁴C/¹²C ratio of a sample from “Modern.” Modern is defined as 95% of the radiocarbon concentration (in AD 1950) of National Bureau of Standards (NBS) Oxalic Acid I (i.e., standard reference materials (SRM) 4990b) normalized to δ¹³C_(VPDB)=−19 per mil (Olsson, The use of Oxalic acid as a Standard. in, Radiocarbon Variations and Absolute Chronology, Nobel Symposium, 12th Proc, John Wiley & Sons, New York (1970)). Mass spectrometry results, for example, measured by ASM, are calculated using the internationally agreed upon definition of 0.95 times the specific activity of NBS Oxalic Acid I (SRM 4990b) normalized to δ¹³C_(VPDB)=−19 per mil. This is equivalent to an absolute (AD 1950) ¹⁴C/¹²C ratio of 1.176±0.010×10⁻¹² (Karlen et al., Arkiv Geofysik, 4:465-471 (1968)). The standard calculations take into account the differential uptake of one isotope with respect to another, for example, the preferential uptake in biological systems of C¹² over C¹³ over C¹⁴, and these corrections are reflected as a Fm corrected for δ¹³.

An oxalic acid standard (SRM 4990b or HOx 1) was made from a crop of 1955 sugar beet. Although there were 1000 lbs made, this oxalic acid standard is no longer commercially available. The Oxalic Acid II standard (HOx 2; N.I.S.T designation SRM 4990 C) was made from a crop of 1977 French beet molasses. In the early 1980's, a group of 12 laboratories measured the ratios of the two standards. The ratio of the activity of Oxalic acid II to 1 is 1.2933±0.001 (the weighted mean). The isotopic ratio of HOx H is −17.8 per mil. ASTM D6866-11 suggests use of the available Oxalic Acid II standard SRM 4990 C (Hox2) for the modern standard (see discussion of original vs. currently available oxalic acid standards in Mann, Radiocarbon, 25(2):519-527 (1983)). A Fm=0% represents the entire lack of carbon-14 atoms in a material, thus indicating a fossil (for example, petroleum based) carbon source. A Fm=100%, after correction for the post-1950 injection of carbon-14 into the atmosphere from nuclear bomb testing, indicates an entirely modern carbon source. As described herein, such a “modern” source includes biobased sources.

As described in ASTM D6866, the percent modern carbon (pMC) can be greater than 100% because of the continuing but diminishing effects of the 1950s nuclear testing programs, which resulted in a considerable enrichment of carbon-14 in the atmosphere as described in ASTM D6866-11. Because all sample carbon-14 activities are referenced to a “pre-bomb” standard, and because nearly all new biobased products are produced in a post-bomb environment, all pMC values (after correction for isotopic fraction) must be multiplied by 0.95 (as of 2010) to better reflect the true biobased content of the sample. A biobased content that is greater than 103% suggests that either an analytical error has occurred, or that the source of biobased carbon is more than several years old.

ASTM D6866 quantifies the biobased content relative to the material's total organic content and does not consider the inorganic carbon and other non-carbon containing substances present. For example, a product that is 50% starch-based material and 50% water would be considered to have a Biobased Content=100% (50% organic content that is 100% biobased) based on ASTM D6866. In another example, a product that is 50% starch-based material, 25% petroleum-based, and 25% water would have a Biobased Content=66.7% (75% organic content but only 50% of the product is biobased). In another example, a product that is 50% organic carbon and is a petroleum-based product would be considered to have a Biobased Content=0% (50% organic carbon but from fossil sources). Thus, based on the well known methods and known standards for determining the biobased content of a compound or material, one skilled in the art can readily determine the biobased content of a compound or material and/or prepared downstream products that utilize a compound or material of the invention having a desired biobased content.

Applications of carbon-14 dating techniques to quantify bio-based content of materials are known in the art (Currie et al., Nuclear Instruments and Methods in Physics Research B, 172:281-287 (2000)). For example, carbon-14 dating has been used to quantify bio-based content in terephthalate-containing materials (Colonna et al., Green Chemistry, 13:2543-2548 (2011)). Notably, polypropylene terephthalate (PPT) polymers derived from renewable 1,3-propanediol and petroleum-derived terephthalic acid resulted in Fm values near 30% (i.e., since 3/11 of the polymeric carbon derives from renewable 1,3-propanediol and 8/11 from the fossil end member terephthalic acid) (Currie et al., supra, 2000). In contrast, polybutylene terephthalate polymer derived from both renewable 1,4-butanediol and renewable terephthalic acid resulted in bio-based content exceeding 90% (Colonna et al., supra, 2011).

Accordingly, in some embodiments, the present invention provides butadiene or 2,4-pentadienoate or a butadiene or 2,4-pentadienoate pathway intermediate that has a carbon-12, carbon-13, and carbon-14 ratio that reflects an atmospheric carbon, also referred to as environmental carbon, uptake source. For example, in some aspects the butadiene or 2,4-pentadienoate or a butadiene or 2,4-pentadienoate pathway intermediate can have an Fm value of at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or as much as 100%. In some such embodiments, the uptake source is CO₂. In some embodiments, the present invention provides butadiene or 2,4-pentadienoate or a butadiene or 2,4-pentadienoate pathway intermediate that has a carbon-12, carbon-13, and carbon-14 ratio that reflects petroleum-based carbon uptake source. In this aspect, the butadiene or 2,4-pentadienoate or a butadiene or 2,4-pentadienoate pathway intermediate can have an Fm value of less than 95%, less than 90%, less than 85%, less than 80% less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10%, less than 5%, less than 2% or less than 1%. In some embodiments, the present invention provides butadiene or 2,4-pentadienoate or a pathway intermediate that has a carbon-12, carbon-13, and carbon-14 ratio that is obtained by a combination of an atmospheric carbon uptake source with a petroleum-based uptake source. Using such a combination of uptake sources is one way by which the carbon-12, carbon-13, and carbon-14 ratio can be varied, and the respective ratios would reflect the proportions of the uptake sources.

Further, the present invention relates to the biologically produced butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate as disclosed herein, and to the products derived therefrom, wherein the butadiene or 2,4-pentadienoate or a butadiene or 2,4-pentadienoate pathway intermediate has a carbon-12, carbon-13, and carbon-14 isotope ratio of about the same value as the CO₂ that occurs in the environment. For example, in some aspects the invention provides bioderived butadiene or 2,4-pentadienoate or a bioderived butadiene or 2,4-pentadienoate intermediate having a carbon-12 versus carbon-13 versus carbon-14 isotope ratio of about the same value as the CO₂ that occurs in the environment, or any of the other ratios disclosed herein. It is understood, as disclosed herein, that a product can have a carbon-12 versus carbon-13 versus carbon-14 isotope ratio of about the same value as the CO₂ that occurs in the environment, or any of the ratios disclosed herein, wherein the product is generated from bioderived butadiene or 2,4-pentadienoate or a bioderived butadiene or 2,4-pentadienoate pathway intermediate as disclosed herein, wherein the bioderived product is chemically modified to generate a final product. Methods of chemically modifying a bioderived product of butadiene or 2,4-pentadienoate, or an intermediate thereof, to generate a desired product are well known to those skilled in the art, as described herein. The invention further provides a polymer, a synthetic rubber, an ABS resin, a chemical, hexamethylenediamine (HIDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, a copolymer, an acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), a styrene-1,3-butadiene latex, a styrene-butadiene latex (SB), a synthetic rubber article, a tire, an adhesive, a seal, a sealant, a coating, a hose, a shoe sole, a polybutadiene rubber, a gasket, a high impact polystyrene (HIPS), a paper coating, a carpet backing, a molded article, a pipe, a telephone, a computer casing, a mobile phone, a radio, an appliance, a foam mattress, a glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), an automotive part, an electrical part, a water system part, polyurethane, a polyurethane-polyurea copolymer, a biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), an elastic fiber, polytetramethylene ether glycol (PTMEG), a spandex fiber, elastane, an industrial solvent, a pharmaceutical, a thermoplastic elastomer (TPE), elastomer polyester, a copolyester ether (COPE), a thermoplastic polyurethane, packaging, a mold extruded product, methylmethacrylate butadiene styrene, a methacrylate butadiene styrene (MBS) resin, a clear resin, a transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) having a carbon-12 versus carbon-13 versus carbon-14 isotope ratio of about the same value as the CO₂ that occurs in the environment, wherein the polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, asphalt modifier, toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) is generated directly from or in combination with bioderived butadiene or 2,4-pentadienoate or a bioderived butadiene or 2,4-pentadienoate pathway intermediate as disclosed herein.

The invention further provides a composition comprising bioderived butadiene or 2,4-pentadienoate, and a compound other than the bioderived butadiene or 2,4-pentadienoate. The compound other than the bioderived product can be a cellular portion, for example, a trace amount of a cellular portion of, or can be fermentation broth or culture medium or a purified or partially purified faction thereof produced in the presence of, a non-naturally occurring microbial organism of the invention having a butadiene or 2,4-pentadienoate pathway. The composition can comprise, for example, a reduced level of a byproduct when produced by an organism having reduced byproduct formation, as disclosed herein. The composition can comprise, for example, bioderived butadiene or 2,4-pentadienoate, or a cell lysate or culture supernatant of a microbial organism of the invention. The compound can also be hydrogen.

Butadiene or 2,4-pentadienoate is a chemical used in commercial and industrial applications. Non-limiting examples of such applications include production of a polymer, a synthetic rubber, an ABS resin, a chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, a copolymer, an acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), a styrene-1,3-butadiene latex, a styrene-butadiene latex (SB), a synthetic rubber article, a tire, an adhesive, a seal, a sealant, a coating, a hose, a shoe sole, a polybutadiene rubber, a gasket, a high impact polystyrene (HIPS), a paper coating, a carpet backing, a molded article, a pipe, a telephone, a computer casing, a mobile phone, a radio, an appliance, a foam mattress, a glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), an automotive part, an electrical part, a water system part, polyurethane, a polyurethane-polyurea copolymer, a biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), an elastic fiber, polytetramethylene ether glycol (PTMEG), a spandex fiber, elastane, an industrial solvent, a pharmaceutical, a thermoplastic elastomer (TPE), elastomer polyester, a copolyester ether (COPE), a thermoplastic polyurethane, packaging, a mold extruded product, methylmethacrylate butadiene styrene, a methacrylate butadiene styrene (MBS) resin, a clear resin, a transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA). Moreover, butadiene or 2,4-pentadienoate is also used as a raw material in the production of a wide range of products including a polymer, a synthetic rubber, an ABS resin, a chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, a copolymer, an acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), a styrene-1,3-butadiene latex, a styrene-butadiene latex (SB), a synthetic rubber article, a tire, an adhesive, a seal, a sealant, a coating, a hose, a shoe sole, a polybutadiene rubber, a gasket, a high impact polystyrene (HIPS), a paper coating, a carpet backing, a molded article, a pipe, a telephone, a computer casing, a mobile phone, a radio, an appliance, a foam mattress, a glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), an automotive part, an electrical part, a water system part, polyurethane, a polyurethane-polyurea copolymer, a biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), an elastic fiber, polytetramethylene ether glycol (PTMEG), a spandex fiber, elastane, an industrial solvent, a pharmaceutical, a thermoplastic elastomer (TPE), elastomer polyester, a copolyester ether (COPE), a thermoplastic polyurethane, packaging, a mold extruded product, methylmethacrylate butadiene styrene, a methacrylate butadiene styrene (MBS) resin, a clear resin, a transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA). Accordingly, in some embodiments, the invention provides biobased polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) comprising one or more bioderived butadiene or 2,4-pentadienoate or bioderived pathway intermediate produced by a non-naturally occurring microorganism of the invention or produced using a method disclosed herein.

As used herein, the term “bioderived” means derived from or synthesized by a biological organism and can be considered a renewable resource since it can be generated by a biological organism. Such a biological organism, in particular the microbial organisms of the invention disclosed herein, can utilize feedstock or biomass, such as, sugars or carbohydrates obtained from an agricultural, plant, bacterial, or animal source. Alternatively, the biological organism can utilize atmospheric carbon. As used herein, the term “biobased” means a product as described above that is composed, in whole or in part, of a bioderived compound of the invention. A biobased or bioderived product is in contrast to a petroleum derived product, wherein such a product is derived from or synthesized from petroleum or a petrochemical feedstock.

In some embodiments, the invention provides a polymer, a synthetic rubber, an ABS resin, a chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, a copolymer, an acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), a styrene-1,3-butadiene latex, a styrene-butadiene latex (SB), a synthetic rubber article, a tire, an adhesive, a seal, a sealant, a coating, a hose, a shoe sole, a polybutadiene rubber, a gasket, a high impact polystyrene (HIPS), a paper coating, a carpet backing, a molded article, a pipe, a telephone, a computer casing, a mobile phone, a radio, an appliance, a foam mattress, a glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), an automotive part, an electrical part, a water system part, polyurethane, a polyurethane-polyurea copolymer, a biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), an elastic fiber, polytetramethylene ether glycol (PTMEG), a spandex fiber, elastane, an industrial solvent, a pharmaceutical, a thermoplastic elastomer (TPE), elastomer polyester, a copolyester ether (COPE), a thermoplastic polyurethane, packaging, a mold extruded product, methylmethacrylate butadiene styrene, a methacrylate butadiene styrene (MBS) resin, a clear resin, a transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) comprising bioderived butadiene or 2,4-pentadienoate or bioderived butadiene or 2,4-pentadienoate pathway intermediate, wherein the bioderived butadiene or 2,4-pentadienoate or bioderived butadiene or 2,4-pentadienoate pathway intermediate includes all or part of the butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate used in the production of a polymer, a synthetic rubber, an ABS resin, a chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, a copolymer, an acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), a styrene-1,3-butadiene latex, a styrene-butadiene latex (SB), a synthetic rubber article, a tire, an adhesive, a seal, a sealant, a coating, a hose, a shoe sole, a polybutadiene rubber, a gasket, a high impact polystyrene (HIPS), a paper coating, a carpet backing, a molded article, a pipe, a telephone, a computer casing, a mobile phone, a radio, an appliance, a foam mattress, a glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), an automotive part, an electrical part, a water system part, polyurethane, a polyurethane-polyurea copolymer, a biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), an elastic fiber, polytetramethylene ether glycol (PTMEG), a spandex fiber, elastane, an industrial solvent, a pharmaceutical, a thermoplastic elastomer (TPE), elastomer polyester, a copolyester ether (COPE), a thermoplastic polyurethane, packaging, a mold extruded product, methylmethacrylate butadiene styrene, a methacrylate butadiene styrene (MBS) resin, a clear resin, a transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA). For example, the final polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) can contain the bioderived butadiene or 2,4-pentadienoate, butadiene or 2,4-pentadienoate pathway intermediate, or a portion thereof that is the result of the manufacturing of a polymer, a synthetic rubber, an ABS resin, a chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, a copolymer, an acrylonitrile 1,3-butadiene styrene (ABS), a styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), a styrene-1,3-butadiene latex, a styrene-butadiene latex (SB), a synthetic rubber article, a tire, an adhesive, a seal, a sealant, a coating, a hose, a shoe sole, a polybutadiene rubber, a gasket, a high impact polystyrene (HIPS), a paper coating, a carpet backing, a molded article, a pipe, a telephone, a computer casing, a mobile phone, a radio, an appliance, a foam mattress, a glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), an automotive part, an electrical part, a water system part, polyurethane, a polyurethane-polyurea copolymer, a biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), an elastic fiber, polytetramethylene ether glycol (PTMEG), a spandex fiber, elastane, an industrial solvent, a pharmaceutical, a thermoplastic elastomer (TPE), elastomer polyester, a copolyester ether (COPE), a thermoplastic polyurethane, packaging, a mold extruded product, methylmethacrylate butadiene styrene, a methacrylate butadiene styrene (MBS) resin, a clear resin, a transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA). Such manufacturing can include chemically reacting the bioderived butadiene or 2,4-pentadienoate or bioderived butadiene or 2,4-pentadienoate pathway intermediate (e.g. chemical conversion, chemical functionalization, chemical coupling, oxidation, reduction, polymerization, copolymerization and the like) into the final polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA). Thus, in some aspects, the invention provides a biobased polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) comprising at least 2%, at least 3%, at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or 100% bioderived butadiene or 2,4-pentadienoate or bioderived butadiene or 2,4-pentadienoate pathway intermediate as disclosed herein.

Additionally, in some embodiments, the invention provides a composition having a bioderived butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate disclosed herein and a compound other than the bioderived butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate. For example, in some aspects, the invention provides a biobased polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) wherein the butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate used in its production is a combination of bioderived and petroleum derived butadiene or 2,4-pentadienoate or butadiene or 2,4-pentadienoate pathway intermediate. For example, a biobased polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) can be produced using 50% bioderived butadiene or 2,4-pentadienoate and 50% petroleum derived butadiene or 2,4-pentadienoate or other desired ratios such as 60%/40%, 70%/30%, 80%/20%, 90%/10%, 95%/5%, 100%/0%, 40%/60%, 30%/70%, 20%/80%, 10%/90% of bioderived/petroleum derived precursors, so long as at least a portion of the product comprises a bioderived product produced by the microbial organisms disclosed herein. It is understood that methods for producing polymer, synthetic rubber, ABS resin, chemical, hexamethylenediamine (HMDA), 1,4-butanediol, tetrahydrofuran (THF), adiponitrile, lauryl lactam, caprolactam, chloroprene, sulfalone, n-octanol, octene-1, polybutadiene, copolymer, acrylonitrile 1,3-butadiene styrene (ABS), styrene-1,3-butadiene rubber (styrene butadiene rubber; SBR), styrene-1,3-butadiene latex, styrene-butadiene latex (SB), synthetic rubber article, tire, adhesive, seal, sealant, coating, hose, shoe sole, polybutadiene rubber, gasket, high impact polystyrene (HIPS), paper coating, carpet backing, molded article, pipe, telephone, computer casing, mobile phone, radio, appliance, foam mattress, glove, footwear, styrene-butadiene block copolymers, an asphalt modifier, a toy, nylon, nylon-6,6, nylon-6,X, polychloroprene (neoprene), thermoplastic, polybutylene terephthalate (PBT), automotive part, electrical part, water system part, polyurethane, polyurethane-polyurea copolymer, biodegradable polymer, PBAT (poly(butylene adipate-co-terephthalate)), PBS (poly(butylene succinate)), elastic fiber, polytetramethylene ether glycol (PTMEG), spandex fiber, elastane, industrial solvent, pharmaceutical, thermoplastic elastomer (TPE), elastomer polyester, copolyester ether (COPE), thermoplastic polyurethane, packaging, mold extruded product, methylmethacrylate butadiene styrene, methacrylate butadiene styrene (MBS) resin, clear resin, transparent thermoplastic, polycarbonate (PC), polyvinyl carbonate (PVC), or polymethyl methacrylate (PMMA) using the bioderived butadiene or 2,4-pentadienoate or bioderived butadiene or 2,4-pentadienoate pathway intermediate of the invention are well known in the art.

The invention further provides bioderived hydrogen produced by culturing anon-naturally culturing microbial organism disclosed herein under conditions and for a sufficient period of time to produce hydrogen. In some embodiments, the invention provides a process for producing hydrogen including (a) culturing a non-naturally culturing microbial organism disclosed herein in a substantially anaerobic culture medium under a condition to produce hydrogen; (b) separating the produced hydrogen from the culture medium; and (c) collecting the separated hydrogen.

In some embodiments, the said condition allowing hydrogen production includes an aqueous environment and a gas phase. The said aqueous environment can contain a liquid feedstock. The liquid feedstock can include a carbon source selected from the group consisting of glucose, xylose, arabinose, galactose, mannose, fructose, sucrose, starch, methonal, and glycerol. In one aspect, the liquid feedstock is supplied continuously. In addition, the gas phase can be continuously flushed with a defined amount of an inert gas, or flushed at defined time points with a defined amount of an inert gas. The aqueous environment also can be continuously bubbled with defined amounts of an inert gas, or flushed at defined time points with a defined amount of an inert gas. In some aspects, the inert gas is nitrogen or argon. In some other embodiments, the produced hydrogen is separated from the culture medium by shaking.

Provided herein are exemplary methods to purify butadiene and hydrogen from the culture medium. In some embodiments, any of the methods or processes described herein further include recovering the co-produced compounds. In some embodiments, any of the methods or processes described herein further include recovering butadiene produced. In some embodiments, any of the methods or processes described herein further include recovering the hydrogen produced. Such methods or processes can include cryogenic membrane, adsorption matrix-based separation methods that are well-known in the art.

The butadiene and/or hydrogen produced using the compositions, methods and processes described herein can be recovered using standard techniques, such as gas stripping, membrane enhanced separation, fractionation, adsorption/desorption, pervaporation, thermal or vacuum desorption of butadiene from a solid phase, or extraction of butadiene immobilized or absorbed to a solid phase with a solvent (see, e.g., U.S. Pat. Nos. 4,703,007, 4,570,029, and 4,740,222, which are each hereby incorporated by reference in their entireties, particularly with respect to hydrogen recovery and purification methods ('222 patent)). Gas stripping involves the removal of butadiene vapor from the fermentation off-gas stream in a continuous manner. Such removal can be achieved in several different ways including, but not limited to, adsorption to a solid phase, partition into a liquid phase, or direct condensation (such as condensation due to exposure to a condensation coil or do to an increase in pressure). In some embodiments, membrane enrichment of a dilute butadiene vapor stream above the dew point of the vapor resulting in the condensation of liquid butadiene. In some embodiments, the butadiene is compressed and condensed.

The recovery of butadiene may involve one step or multiple steps. In some embodiments, the removal of butadiene vapor from the fermentation off-gas and the conversion of butadiene to a liquid phase are performed simultaneously. For example, butadiene can be directly condensed from the off-gas stream to form a liquid. In some embodiments, the removal of butadiene vapor from the fermentation off-gas and the conversion of butadiene to a liquid phase are performed sequentially. For example, butadiene may be adsorbed to a solid phase and then extracted from the solid phase with a solvent.

The recovery of hydrogen may involve one step or multiple steps. In some embodiments, the removal of hydrogen gas from the fermentation off-gas and the conversion of hydrogen to a liquid phase are performed simultaneously. In some embodiments, the removal of hydrogen gas from the fermentation off-gas and the conversion of hydrogen to a liquid phase are performed sequentially. For example, hydrogen may be adsorbed to a solid phase and then desorbed from the solid phase by a ressure swing. In some embodiments, recovered hydrogen gas is concentrated and compressed.

In some embodiments, any of the methods described herein further include purifying the hydrogen. For example, the hydrogen produced using the compositions and methods described herein can be purified using standard techniques. Purification refers to a process through which hydrogen is separated from one or more components that are present when the hydrogen is produced. In some embodiments, the hydrogen is obtained as a substantially pure gas. In some embodiments, the hydrogen is obtained as a substantially pure liquid. Examples of purification methods include (i) cryogenic condensation and (ii) solid matrix adsorption. As used herein, “purified hydrogen” means hydrogen that has been separated from one or more components that are present when the hydrogen is produced. In some embodiments, the hydrogen is at least about 20%, by weight, free from other components that are present when the hydrogen is produced. In various embodiments, the hydrogen is at least or about 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 90%, 95%, or 99%, by weight, pure. Purity can be assayed by any appropriate method, e.g., by column chromatography or GC-MS analysis.

In some embodiments, at least a portion of the gas phase remaining after one or more recovery steps for the removal of butadiene is recycled by introducing the gas phase into a cell culture system (such as a fermentor) for the production of butadiene.

A bioderived composition from a fermentor off-gas may contain butadiene with volatile impurities and bio-byproduct impurities. In some embodiments, butadiene from a fermentor off-gas can be purified using a method comprising. (a) contacting the fermentor off-gas with a solvent in a first column to form a butadiene-rich solution comprising the solvent, a major portion of the butadiene and a major portion of the bio-byproduct impurity; and a vapor comprising a major portion of the volatile impurity; (b) transferring the butadiene-rich solution from the first column to a second column; and (c) stripping butadiene from the butadiene-rich solution in the second column to form: an butadiene-lean solution comprising a major portion of the bio-byproduct impurity; and a purified butadiene.

Separation of hydrogen from other gaseous products such as butadiene, CO2 can be accomplished by well-known methods such as pressure-swing adsorption and membrane-based methods. There are several types of membranes: gas-diffusion, ion conducting, and catalytic membranes. Apparatus and methods for separation of H2 from CO2 produced during fermentation is known in the art (see, e.g., US2010/02483181, which is incorporated herein by reference) and can be used in the methods and processes described herein.

The culture conditions can include, for example, liquid culture procedures as well as fermentation and other large scale culture procedures. As described herein, particularly useful yields of the biosynthetic products of the invention can be obtained under anaerobic or substantially anaerobic culture conditions.

As described herein, one exemplary growth condition for achieving biosynthesis of butadiene or 2,4-pentadienoate includes anaerobic culture or fermentation conditions. In certain embodiments, the non-naturally occurring microbial organisms of the invention can be sustained, cultured or fermented under anaerobic or substantially anaerobic conditions. Briefly, an anaerobic condition refers to an environment devoid of oxygen. Substantially anaerobic conditions include, for example, a culture, batch fermentation or continuous fermentation such that the dissolved oxygen concentration in the medium remains between 0 and 10% of saturation. Substantially anaerobic conditions also includes growing or resting cells in liquid medium or on solid agar inside a sealed chamber maintained with an atmosphere of less than 1% oxygen. The percent of oxygen can be maintained by, for example, sparging the culture with an N₂/CO₂ mixture or other suitable non-oxygen gas or gases.

The culture conditions described herein can be scaled up and grown continuously for manufacturing of butadiene or 2,4-pentadienoate. Exemplary growth procedures include, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. All of these processes are well known in the art. Fermentation procedures are particularly useful for the biosynthetic production of commercial quantities of butadiene or 2,4-pentadienoate. Generally, and as with non-continuous culture procedures, the continuous and/or near-continuous production of butadiene or 2,4-pentadienoate will include culturing a non-naturally occurring butadiene or 2,4-pentadienoate producing organism of the invention in sufficient nutrients and medium to sustain and/or nearly sustain growth in an exponential phase. Continuous culture under such conditions can include, for example, growth or culturing for 1 day, 2, 3, 4, 5, 6 or 7 days or more. Additionally, continuous culture can include longer time periods of 1 week, 2, 3, 4 or 5 or more weeks and up to several months. Alternatively, organisms of the invention can be cultured for hours, if suitable for a particular application. It is to be understood that the continuous and/or near-continuous culture conditions also can include all time intervals in between these exemplary periods. It is further understood that the time of culturing the microbial organism of the invention is for a sufficient period of time to produce a sufficient amount of product for a desired purpose.

Fermentation procedures are well known in the art. Briefly, fermentation for the biosynthetic production of butadiene or 2,4-pentadienoate can be utilized in, for example, fed-batch fermentation and batch separation; fed-batch fermentation and continuous separation, or continuous fermentation and continuous separation. Examples of batch and continuous fermentation procedures are well known in the art.

In addition to the above fermentation procedures using the butadiene or 2,4-pentadienoate producers of the invention for continuous production of substantial quantities of butadiene or 2,4-pentadienoate, the butadiene or 2,4-pentadienoate producers also can be, for example, simultaneously subjected to chemical synthesis and/or enzymatic procedures to convert the product to other compounds or the product can be separated from the fermentation culture and sequentially subjected to chemical and/or enzymatic conversion to convert the product to other compounds, if desired.

To generate better producers, metabolic modeling can be utilized to optimize growth conditions. Modeling can also be used to design gene knockouts that additionally optimize utilization of the pathway (see, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and U.S. Pat. No. 7,127,379). Modeling analysis allows reliable predictions of the effects on cell growth of shifting the metabolism towards more efficient production of butadiene or 2,4-pentadienoate.

One computational method for identifying and designing metabolic alterations favoring biosynthesis of a desired product is the OptKnock computational framework (Burgard et al., Biotechnol. Bioeng. 84:647-657 (2003)). OptKnock is a metabolic modeling and simulation program that suggests gene deletion or disruption strategies that result in genetically stable microorganisms which overproduce the target product. Specifically, the framework examines the complete metabolic and/or biochemical network of a microorganism in order to suggest genetic manipulations that force the desired biochemical to become an obligatory byproduct of cell growth. By coupling biochemical production with cell growth through strategically placed gene deletions or other functional gene disruption, the growth selection pressures imposed on the engineered strains after long periods of time in a bioreactor lead to improvements in performance as a result of the compulsory growth-coupled biochemical production. Lastly, when gene deletions are constructed there is a negligible possibility of the designed strains reverting to their wild-type states because the genes selected by OptKnock are to be completely removed from the genome. Therefore, this computational methodology can be used to either identify alternative pathways that lead to biosynthesis of a desired product or used in connection with the non-naturally occurring microbial organisms for further optimization of biosynthesis of a desired product.

Briefly, OptKnock is a term used herein to refer to a computational method and system for modeling cellular metabolism. The OptKnock program relates to a framework of models and methods that incorporate particular constraints into flux balance analysis (FBA) models. These constraints include, for example, qualitative kinetic information, qualitative regulatory information, and/or DNA microarray experimental data. OptKnock also computes solutions to various metabolic problems by, for example, tightening the flux boundaries derived through flux balance models and subsequently probing the performance limits of metabolic networks in the presence of gene additions or deletions. OptKnock computational framework allows the construction of model formulations that allow an effective query of the performance limits of metabolic networks and provides methods for solving the resulting mixed-integer linear programming problems. The metabolic modeling and simulation methods referred to herein as OptKnock are described in, for example, U.S. publication 2002/0168654, filed Jan. 10, 2002, in International Patent No. PCT/US02/00660, filed Jan. 10, 2002, and U.S. publication 2009/0047719, filed Aug. 10, 2007.

Another computational method for identifying and designing metabolic alterations favoring biosynthetic production of a product is a metabolic modeling and simulation system termed SimPheny®. This computational method and system is described in, for example, U.S. publication 2003/0233218, filed Jun. 14, 2002, and in International Patent Application No. PCT/US03/18838, filed Jun. 13, 2003. SimPheny® is a computational system that can be used to produce a network model in silico and to simulate the flux of mass, energy or charge through the chemical reactions of a biological system to define a solution space that contains any and all possible functionalities of the chemical reactions in the system, thereby determining a range of allowed activities for the biological system. This approach is referred to as constraints-based modeling because the solution space is defined by constraints such as the known stoichiometry of the included reactions as well as reaction thermodynamic and capacity constraints associated with maximum fluxes through reactions. The space defined by these constraints can be interrogated to determine the phenotypic capabilities and behavior of the biological system or of its biochemical components.

These computational approaches are consistent with biological realities because biological systems are flexible and can reach the same result in many different ways. Biological systems are designed through evolutionary mechanisms that have been restricted by fundamental constraints that all living systems must face. Therefore, constraints-based modeling strategy embraces these general realities. Further, the ability to continuously impose further restrictions on a network model via the tightening of constraints results in a reduction in the size of the solution space, thereby enhancing the precision with which physiological performance or phenotype can be predicted.

Given the teachings and guidance provided herein, those skilled in the art will be able to apply various computational frameworks for metabolic modeling and simulation to design and implement biosynthesis of a desired compound in host microbial organisms. Such metabolic modeling and simulation methods include, for example, the computational systems exemplified above as SimPheny® and OptKnock. For illustration of the invention, some methods are described herein with reference to the OptKnock computation framework for modeling and simulation. Those skilled in the art will know how to apply the identification, design and implementation of the metabolic alterations using OptKnock to any of such other metabolic modeling and simulation computational frameworks and methods well known in the art.

The methods described above will provide one set of metabolic reactions to disrupt. Elimination of each reaction within the set or metabolic modification can result in a desired product as an obligatory product during the growth phase of the organism. Because the reactions are known, a solution to the bilevel OptKnock problem also will provide the associated gene or genes encoding one or more enzymes that catalyze each reaction within the set of reactions. Identification of a set of reactions and their corresponding genes encoding the enzymes participating in each reaction is generally an automated process, accomplished through correlation of the reactions with a reaction database having a relationship between enzymes and encoding genes.

Once identified, the set of reactions that are to be disrupted in order to achieve production of a desired product are implemented in the target cell or organism by functional disruption of at least one gene encoding each metabolic reaction within the set. One particularly useful means to achieve functional disruption of the reaction set is by deletion of each encoding gene. However, in some instances, it can be beneficial to disrupt the reaction by other genetic aberrations including, for example, mutation, deletion of regulatory regions such as promoters or cis binding sites for regulatory factors, or by truncation of the coding sequence at any of a number of locations. These latter aberrations, resulting in less than total deletion of the gene set can be useful, for example, when rapid assessments of the coupling of a product are desired or when genetic reversion is less likely to occur.

To identify additional productive solutions to the above described bilevel OptKnock problem which lead to further sets of reactions to disrupt or metabolic modifications that can result in the biosynthesis, including growth-coupled biosynthesis of a desired product, an optimization method, termed integer cuts, can be implemented. This method proceeds by iteratively solving the OptKnock problem exemplified above with the incorporation of an additional constraint referred to as an integer cut at each iteration. Integer cut constraints effectively prevent the solution procedure from choosing the exact same set of reactions identified in any previous iteration that obligatorily couples product biosynthesis to growth. For example, if a previously identified growth-coupled metabolic modification specifies reactions 1, 2, and 3 for disruption, then the following constraint prevents the same reactions from being simultaneously considered in subsequent solutions. The integer cut method is well known in the art and can be found described in, for example, Burgard et al., Biotechnol. Prog. 17:791-797 (2001). As with all methods described herein with reference to their use in combination with the OptKnock computational framework for metabolic modeling and simulation, the integer cut method of reducing redundancy in iterative computational analysis also can be applied with other computational frameworks well known in the art including, for example, SimPheny®.

The methods exemplified herein allow the construction of cells and organisms that biosynthetically produce a desired product, including the obligatory coupling of production of a target biochemical product to growth of the cell or organism engineered to harbor the identified genetic alterations. Therefore, the computational methods described herein allow the identification and implementation of metabolic modifications that are identified by an in silico method selected from OptKnock or SimPheny®. The set of metabolic modifications can include, for example, addition of one or more biosynthetic pathway enzymes and/or functional disruption of one or more metabolic reactions including, for example, disruption by gene deletion.

As discussed above, the OptKnock methodology was developed on the premise that mutant microbial networks can be evolved towards their computationally predicted maximum-growth phenotypes when subjected to long periods of growth selection. In other words, the approach leverages an organism's ability to self-optimize under selective pressures. The OptKnock framework allows for the exhaustive enumeration of gene deletion combinations that force a coupling between biochemical production and cell growth based on network stoichiometry. The identification of optimal gene/reaction knockouts requires the solution of a bilevel optimization problem that chooses the set of active reactions such that an optimal growth solution for the resulting network overproduces the biochemical of interest (Burgard et al., Biotechnol. Bioeng. 84:647-657 (2003)).

An in silico stoichiometric model of E. coli metabolism can be employed to identify essential genes for metabolic pathways as exemplified previously and described in, for example, U.S. patent publications US 2002/0012939, US 2003/0224363, US 2004/0029149, US 2004/0072723, US 2003/0059792, US 2002/0168654 and US 2004/0009466, and in U.S. Pat. No. 7,127,379. As disclosed herein, the OptKnock mathematical framework can be applied to pinpoint gene deletions leading to the growth-coupled production of a desired product. Further, the solution of the bilevel OptKnock problem provides only one set of deletions. To enumerate all meaningful solutions, that is, all sets of knockouts leading to growth-coupled production formation, an optimization technique, termed integer cuts, can be implemented. This entails iteratively solving the OptKnock problem with the incorporation of an additional constraint referred to as an integer cut at each iteration, as discussed above.

Employing the methods exemplified above, the methods of the invention allow the construction of cells and organisms that increase production of a desired product, for example, by coupling the production of a desired product to growth of the cell or organism engineered to harbor the identified genetic alterations. As disclosed herein, metabolic alterations have been identified that couple the production of butadiene or 2,4-pentadienoate to growth of the organism. Microbial organism strains constructed with the identified metabolic alterations produce elevated levels, relative to the absence of the metabolic alterations, of butadiene or 2,4-pentadienoate during the exponential growth phase. These strains can be beneficially used for the commercial production of butadiene or 2,4-pentadienoate in continuous fermentation process without being subjected to the negative selective pressures described previously. Although exemplified herein as metabolic alterations, in particular one or more gene disruptions, that confer growth coupled production of butadiene or 2,4-pentadienoate, it is understood that any gene disruption that increases the production of butadiene or 2,4-pentadienoate can be introduced into a host microbial organism, as desired.

Therefore, the methods of the invention provide a set of metabolic modifications that are identified by an in silico method such as OptKnock. The set of metabolic modifications can include functional disruption of one or more metabolic reactions including, for example, disruption by gene deletion. For butadiene or 2,4-pentadienoate production, metabolic modifications can be selected from the set of metabolic modifications listed in FIG. 3.

Also provided is a method of producing anon-naturally occurring microbial organisms having stable growth-coupled production of butadiene or 2,4-pentadienoate. The method can include identifying in silico a set of metabolic modifications that increase production of butadiene or 2,4-pentadienoate, for example, increase production during exponential growth; genetically modifying an organism to contain the set of metabolic modifications that increase production of butadiene or 2,4-pentadienoate, and culturing the genetically modified organism. If desired, culturing can include adaptively evolving the genetically modified organism under conditions requiring production of butadiene or 2,4-pentadienoate. The methods of the invention are applicable to bacterium, yeast and fungus as well as a variety of other cells and microorganism, as disclosed herein.

Thus, the invention provides anon-naturally occurring microbial organism comprising one or more gene disruptions that confer increased production of butadiene or 2,4-pentadienoate. In one embodiment, the one or more gene disruptions confer growth-coupled production of butadiene or 2,4-pentadienoate, and can, for example, confer stable growth-coupled production of butadiene or 2,4-pentadienoate. In another embodiment, the one or more gene disruptions can confer obligatory coupling of butadiene or 2,4-pentadienoate production to growth of the microbial organism. Such one or more gene disruptions reduce the activity of the respective one or more encoded enzymes.

The non-naturally occurring microbial organism can have one or more gene disruptions included in a metabolic modification listed in FIG. 3. As disclosed herein, the one or more gene disruptions can be a deletion. Such non-naturally occurring microbial organisms of the invention include bacteria, yeast, fungus, or any of a variety of other microorganisms applicable to fermentation processes, as disclosed herein.

Thus, the invention provides anon-naturally occurring microbial organism, comprising one or more gene disruptions, where the one or more gene disruptions occur in genes encoding proteins or enzymes where the one or more gene disruptions confer increased production of butadiene or 2,4-pentadienoate in the organism. The production of butadiene or 2,4-pentadienoate can be growth-coupled or not growth-coupled. In a particular embodiment, the production of butadiene or 2,4-pentadienoate can be obligatorily coupled to growth of the organism, as disclosed herein.

In some embodiments, the invention provides a non-naturally occurring microbial organism as described herein, wherein the microbial organism further includes attenuation of one or more endogenous enzymes, which enhances carbon flux through acetyl-CoA. For example, in some aspects, the endogenous enzyme can be selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof. Accordingly, in some aspects, the attenuation is of the endogenous enzyme DHA kinase. In some aspects, the attenuation is of the endogenous enzyme methanol oxidase. In some aspects, the attenuation is of the endogenous enzyme PQQ-dependent methanol dehydrogenase. In some aspects, the attenuation is of the endogenous enzyme DHA synthase. The invention also provides a microbial organism wherein attenuation is of any combination of two or three endogenous enzymes described herein. For example, a microbial organism of the invention can include attenuation of DHA kinase and DHA synthase, or alternatively methanol oxidase and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and DHA synthase. The invention also provides a microbial organism wherein attenuation is of all endogenous enzymes described herein. For example, in some aspects, a microbial organism described herein includes attenuation of DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase and DHA synthase.

In some embodiments, the invention provides a non-naturally occurring microbial organism as described herein, wherein the microbial organism further includes attenuation of one or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway. Examples of these endogenous enzymes are disclosed in FIG. 3. It is understood that a person skilled in the art would be able to readily identify enzymes of such competing pathways. Competing pathways can be dependent upon the host microbial organism and/or the exogenous nucleic acid introduced into the microbial organism as described herein. Accordingly, in some aspects of the invention, the microbial organism includes attenuation of one, two, three, four, five, six, seven, eight, nine, ten or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway.

In some embodiments, the invention provides a non-naturally occurring microbial organism as described herein, wherein the microbial organism further includes a gene disruption of one or more endogenous nucleic acids encoding enzymes, which enhances carbon flux through acetyl-CoA. For example, in some aspects, the endogenous enzyme can be selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof. According, in some aspects, the gene disruptiondisruption is of an endogenous nucleic acid encoding the enzyme DHA kinase. In some aspects, the gene disruptiondisruption is of an endogenous nucleic acid encoding the enzyme methanol oxidase. In some aspects, the gene disruptiondisruption is of an endogenous nucleic acid encoding the enzyme PQQ-dependent methanol dehydrogenase. In some aspects, the gene disruption is of an endogenous nucleic acid encoding the enzyme DHA synthase. The invention also provides a microbial organism wherein the gene disruption is of any combination of two or three nucleic acids encoding endogenous enzymes described herein. For example, a microbial organism of the invention can include a gene disruption of DHA kinase and DHA synthase, or alternatively methanol oxidase and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and PQQ-dependent methanol dehydrogenase, or alternatively DHA kinase, methanol oxidase, and DHA synthase. The invention also provides a microbial organism wherein all endogenous nucleic acids encoding enzymes described herein are disrupted. For example, in some aspects, a microbial organism described herein includes disruption of DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase and DHA synthase.

In some embodiments, the invention provides a non-naturally occurring microbial organism as described herein, wherein the microbial organism further includes a gene disruption of one or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway. Examples of these endogenous enzymes are disclosed in FIG. 3. It is understood that a person skilled in the art would be able to readily identify enzymes of such competing pathways. Competing pathways can be dependent upon the host microbial organism and/or the exogenous nucleic acid introduced into the microbial organism as described herein. Accordingly, in some aspects of the invention, the microbial organism includes a gene disruption of one, two, three, four, five, six, seven, eight, nine, ten or more endogenous nucleic acids encoding enzymes of a competing formaldehyde assimilation or dissimilation pathway.

The invention provides non naturally occurring microbial organisms having genetic alterations such as gene disruptions that increase production of butadiene or 2,4-pentadienoate, for example, growth-coupled production of butadiene or 2,4-pentadienoate. Product production can be, for example, obligatorily linked to the exponential growth phase of the microorganism by genetically altering the metabolic pathways of the cell, as disclosed herein. The genetic alterations can increase the production of the desired product or even make the desired product an obligatory product during the growth phase. Sets of metabolic alterations or transformations that result in increased production and elevated levels of butadiene or 2,4-pentadienoate biosynthesis are exemplified in FIG. 3. Each alteration within a set corresponds to the requisite metabolic reaction that should be functionally disrupted. Functional disruption of all reactions within each set can result in the increased production of butadiene or 2,4-pentadienoate by the engineered strain during the growth phase. The corresponding reactions to the referenced alterations can be found in FIG. 3, and the gene or genes that encode enzymes or proteins that carry out the reactions are set forth in FIG. 3.

For example, for each strain exemplified in FIG. 3, the metabolic alterations that can be generated for butadiene or 2,4-pentadienoate production are shown with “X” markings. These alterations include the functional disruption of the reactions shown in FIG. 3. Each of these non-naturally occurring alterations result in increased production and an enhanced level of butadiene or 2,4-pentadienoate production, for example, during the exponential growth phase of the microbial organism, compared to a strain that does not contain such metabolic alterations, under appropriate culture conditions. Appropriate conditions include, for example, those disclosed herein, including conditions such as particular carbon sources or reactant availabilities and/or adaptive evolution.

Given the teachings and guidance provided herein, those skilled in the art will understand that to introduce a metabolic alteration such as attenuation of an enzyme, it can be necessary to disrupt the catalytic activity of the one or more enzymes involved in the reaction. Alternatively, a metabolic alteration can include disrupting expression of a regulatory protein or cofactor necessary for enzyme activity or maximal activity. Furthermore, genetic loss of a cofactor necessary for an enzymatic reaction can also have the same effect as a disruption of the gene encoding the enzyme. Disruption can occur by a variety of methods including, for example, deletion of an encoding gene or incorporation of a genetic alteration in one or more of the encoding gene sequences. The encoding genes targeted for disruption can be one, some, or all of the genes encoding enzymes involved in the catalytic activity. For example, where a single enzyme is involved in a targeted catalytic activity, disruption can occur by a genetic alteration that reduces or eliminates the catalytic activity of the encoded gene product. Similarly, where the single enzyme is multimeric, including heteromeric, disruption can occur by a genetic alteration that reduces or destroys the function of one or all subunits of the encoded gene products. Destruction of activity can be accomplished by loss of the binding activity of one or more subunits required to form an active complex, by destruction of the catalytic subunit of the multimeric complex or by both. Other functions of multimeric protein association and activity also can be targeted in order to disrupt a metabolic reaction of the invention. Such other functions are well known to those skilled in the art. Similarly, a target enzyme activity can be reduced or eliminated by disrupting expression of a protein or enzyme that modifies and/or activates the target enzyme, for example, a molecule required to convert an apoenzyme to a holoenzyme. Further, some or all of the functions of a single polypeptide or multimeric complex can be disrupted according to the invention in order to reduce or abolish the catalytic activity of one or more enzymes involved in a reaction or metabolic modification of the invention. Similarly, some or all of enzymes involved in a reaction or metabolic modification of the invention can be disrupted so long as the targeted reaction is reduced or eliminated.

Given the teachings and guidance provided herein, those skilled in the art also will understand that an enzymatic reaction can be disrupted by reducing or eliminating reactions encoded by a common gene and/or by one or more orthologs of that gene exhibiting similar or substantially the same activity. Reduction of both the common gene and all orthologs can lead to complete abolishment of any catalytic activity of a targeted reaction. However, disruption of either the common gene or one or more orthologs can lead to a reduction in the catalytic activity of the targeted reaction sufficient to promote coupling of growth to product biosynthesis. Exemplified herein are both the common genes encoding catalytic activities for a variety of metabolic modifications as well as their orthologs. Those skilled in the art will understand that disruption of some or all of the genes encoding a enzyme of a targeted metabolic reaction can be practiced in the methods of the invention and incorporated into the non-naturally occurring microbial organisms of the invention in order to achieve the increased production of butadiene or 2,4-pentadienoate or growth-coupled product production.

Given the teachings and guidance provided herein, those skilled in the art also will understand that enzymatic activity or expression can be attenuated using well known methods. Reduction of the activity or amount of an enzyme can mimic complete disruption of a gene if the reduction causes activity of the enzyme to fall below a critical level that is normally required for a pathway to function. Reduction of enzymatic activity by various techniques rather than use of a gene disruption can be important for an organism's viability. Methods of reducing enzymatic activity that result in similar or identical effects of a gene disruption include, but are not limited to: reducing gene transcription or translation; destabilizing mRNA, protein or catalytic RNA; and mutating a gene that affects enzyme activity or kinetics (See, Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Ed., Cold Spring Harbor Laboratory, New York (2001); and Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1999). Natural or imposed regulatory controls can also accomplish enzyme attenuation including: promoter replacement (See, Wang et al., Mol. Biotechnol. 52(2):300-308 (2012)); loss or alteration of transcription factors (Dietrick et al., Annu. Rev. Biochem. 79:563-590 (2010); and Simicevic et al., Mol. Biosyst. 6(3):462-468 (2010)); introduction of inhibitory RNAs or peptides such as siRNA, antisense RNA, RNA or peptide/small-molecule binding aptamers, ribozymes, aptazymes and riboswitches (Wieland et al., Methods 56(3):351-357 (2012); O'Sullivan, Anal. Bioanal. Chem. 372(1):44-48 (2002); and Lee et al., Curr. Opin. Biotechnol. 14(5):505-511 (2003)); and addition of drugs or other chemicals that reduce or disrupt enzymatic activity such as an enzyme inhibitor, an antibiotic or a target-specific drug.

One skilled in the art will also understand and recognize that attenuation of an enzyme can be done at various levels. For example, at the gene level, a mutation causing a partial or complete null phenotype, such as a gene disruption, or a mutation causing epistatic genetic effects that mask the activity of a gene product (Miko, Nature Education 1 (1) (2008)), can be used to attenuate an enzyme. At the gene expression level, methods for attenuation include: coupling transcription to an endogenous or exogenous inducer, such as isopropylthio-β-galactoside (IPTG), then adding low amounts of inducer or no inducer during the production phase (Donovan et al., J Ind. Microbiol. 16(3):145-154 (1996); and Hansen et al., Curr. Microbiol. 36(6):341-347 (1998)); introducing or modifying a positive or a negative regulator of a gene; modify histone acetylation/deacetylation in a eukaryotic chromosomal region where a gene is integrated (Yang et al., Curr. Opin. Genet. Dev. 13(2):143-153 (2003) and Kurdistani et al., Nat. Rev. Mol. Cell Biol. 4(4):276-284 (2003)); introducing a transposition to disrupt a promoter or a regulatory gene (Bleykasten-Brosshans et al., C. R Biol. 33(8-9):679-686 (2011); and McCue et al., PLoS Genet. 8(2):e1002474 (2012)); flipping the orientation of a transposable element or promoter region so as to modulate gene expression of an adjacent gene (Wang et al., Genetics 120(4):875-885 (1988); Hayes, Annu. Rev. Genet. 37:3-29 (2003); in a diploid organism, deleting one allele resulting in loss of heterozygosity (Daigaku et al., Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 600(1-2)177-183 (2006)); introducing nucleic acids that increase RNA degradation (Houseley et al., Cell, 136(4):763-776 (2009); or in bacteria, for example, introduction of a transfer-messenger RNA (tmRNA) tag, which can lead to RNA degradation and ribosomal stalling (Sunohara et al., RNA 10(3):378-386 (2004); and Sunohara et al., J. Biol. Chem. 279:15368-15375 (2004)). At the translational level, attenuation can include: introducing rare codons to limit translation (Angov, Biotechnol. J. 6(6):650-659 (2011)); introducing RNA interference molecules that block translation (Castel et al., Nat. Rev. Genet. 14(2):100-112 (2013); and Kawasaki et al., Curr. Opin. Mol. Ther. 7(2):125-131(2005); modifying regions outside the coding sequence, such as introducing secondary structure into an untranslated region (UTR) to block translation or reduce efficiency of translation (Ringnér et al., PLoS Comput. Biol. 1(7):e72 (2005)); adding RNAase sites for rapid transcript degradation (Pasquinelli, Nat. Rev. Genet. 13(4):271-282 (2012); and Arraiano et al., FEMS Microbiol. Rev. 34(5):883-932 (2010); introducing antisense RNA oligomers or antisense transcripts (Nashizawa et al., Front. Biosci. 17:938-958 (2012)); introducing RNA or peptide aptamers, ribozymes, aptazymes, riboswitches (Wieland et al., Methods 56(3):351-357 (2012); O'Sullivan, Anal. Bioanal. Chem. 372(1):44-48 (2002); and Lee et al., Curr. Opin. Biotechnol. 14(5):505-511(2003)); or introducing translational regulatory elements involving RNA structure that can prevent or reduce translation that can be controlled by the presence or absence of small molecules (Araujo et al., Comparative and Functional Genomics, Article ID 475731, 8 pages (2012)). At the level of enzyme localization and/or longevity, enzyme attenuation can include: adding a degradation tag for faster protein turnover (Hochstrasser, Annual Rev. Genet. 30:405-439 (1996); and Yuan et al., PLoS One 8(4):e62529 (2013)); or adding a localization tag that results in the enzyme being secreted or localized to a subcellular compartment in a eukaryotic cell, where the enzyme would not be able to react with its normal substrate (Nakai et al. Genomics 14(4):897-911(1992); and Russell et al., J. Bact. 189(21)7581-7585 (2007)). At the level of post-translational regulation, enzyme attenuation can include: increasing intracellular concentration of known inhibitors; or modifying post-translational modified sites (Mann et al., Nature Biotech. 21:255-261(2003)). At the level of enzyme activity, enzyme attenuation can include: adding an endogenous or an exogenous inhibitor, such as an enzyme inhibitor, an antibiotic or a target-specific drug, to reduce enzyme activity; limiting availability of essential cofactors, such as vitamin B12, for an enzyme that requires the cofactor; chelating a metal ion that is required for enzyme activity; or introducing a dominant negative mutation. The applicability of a technique for attenuation described above can depend upon whether a given host microbial organism is prokaryotic or eukaryotic, and it is understand that a determination of what is the appropriate technique for a given host can be readily made by one skilled in the art.

In some embodiments, microaerobic designs can be used based on the growth-coupled formation of the desired product. To examine this, production cones can be constructed for each strategy by first maximizing and, subsequently minimizing the product yields at different rates of biomass formation feasible in the network. If the rightmost boundary of all possible phenotypes of the mutant network is a single point, it implies that there is a unique optimum yield of the product at the maximum biomass formation rate possible in the network. In other cases, the rightmost boundary of the feasible phenotypes is a vertical line, indicating that at the point of maximum biomass the network can make any amount of the product in the calculated range, including the lowest amount at the bottommost point of the vertical line. Such designs are given a low priority.

The butadiene or 2,4-pentadienoate-production strategies identified by the methods disclosed herein such as the OptKnock framework are generally ranked on the basis of their (i) theoretical yields, and (ii) growth-coupled butadiene or 2,4-pentadienoate formation characteristics. For the designs disclosed herein, the genes that can be disrupted to increase production of butadiene or 2,4-pentadienoate are shown in FIG. 3.

Accordingly, the invention also provides anon-naturally occurring microbial organism having a set of metabolic modifications coupling butadiene or 2,4-pentadienoate production to growth of the organism, where the set of metabolic modifications includes disruption of one or more genes selected from the set of genes encoding proteins as in FIG. 3.

Each of the strains can be supplemented with additional deletions if it is determined that the strain designs do not sufficiently increase the production of butadiene or 2,4-pentadienoate and/or couple the formation of the product with biomass formation. Alternatively, some other enzymes not known to possess significant activity under the growth conditions can become active due to adaptive evolution or random mutagenesis. Such activities can also be knocked out. However, the list of gene deletion sets disclosed herein allows the construction of strains exhibiting high-yield production of butadiene or 2,4-pentadienoate, including growth-coupled production of butadiene or 2,4-pentadienoate.

Butadiene or 2,4-pentadienoate can be harvested or isolated at any time point during the culturing of the microbial organism, for example, in a continuous and/or near-continuous culture period, as disclosed herein. Generally, the longer the microorganisms are maintained in a continuous and/or near-continuous growth phase, the proportionally greater amount of butadiene or 2,4-pentadienoate can be produced.

Therefore, the invention additionally provides a method for producing butadiene or 2,4-pentadienoate that includes culturing anon-naturally occurring microbial organism having one or more gene disruptions, as disclosed herein. The disruptions can occur in one or more genes encoding an enzyme that increases production of butadiene or 2,4-pentadienoate, including optionally coupling butadiene or 2,4-pentadienoate production to growth of the microorganism when the gene disruption reduces or eliminates an activity of the enzyme. For example, the disruptions can confer stable growth-coupled production of butadiene or 2,4-pentadienoate onto the non-naturally microbial organism.

In some embodiments, the gene disruption can include a complete gene deletion. In some embodiments other methods to disrupt a gene include, for example, frameshifting by omission or addition of oligonucleotides or by mutations that render the gene inoperable. One skilled in the art will recognize the advantages of gene deletions, however, because of the stability it confers to the non-naturally occurring organism from reverting to a parental phenotype in which the gene disruption has not occurred. In particular, the gene disruptions are selected from the gene sets as disclosed herein.

Once computational predictions are made of gene sets for disruption to increase production of butadiene or 2,4-pentadienoate, the strains can be constructed, evolved, and tested. Gene disruptions, including gene deletions, are introduced into host organism by methods well known in the art. A particularly useful method for gene disruption is by homologous recombination, as disclosed herein.

The engineered strains can be characterized by measuring the growth rate, the substrate uptake rate, and/or the product/byproduct secretion rate. Cultures can be grown and used as inoculum for a fresh batch culture for which measurements are taken during exponential growth. The growth rate can be determined by measuring optical density using a spectrophotometer (A600). Concentrations of glucose and other organic acid byproducts in the culture supernatant can be determined by well known methods such as HPLC, GC-MS or other well known analytical methods suitable for the analysis of the desired product, as disclosed herein, and used to calculate uptake and secretion rates.

Strains containing gene disruptions can exhibit suboptimal growth rates until their metabolic networks have adjusted to their missing functionalities. To assist in this adjustment, the strains can be adaptively evolved. By subjecting the strains to adaptive evolution, cellular growth rate becomes the primary selection pressure and the mutant cells are compelled to reallocate their metabolic fluxes in order to enhance their rates of growth. This reprogramming of metabolism has been recently demonstrated for several E. coli mutants that had been adaptively evolved on various substrates to reach the growth rates predicted a priori by an in silico model (Fong and Palsson, Nat. Genet. 36:1056-1058 (2004)). The growth improvements brought about by adaptive evolution can be accompanied by enhanced rates of butadiene or 2,4-pentadienoate production. The strains are generally adaptively evolved in replicate, running in parallel, to account for differences in the evolutionary patterns that can be exhibited by a host organism (Fong and Palsson, Nat. Genet. 36:1056-1058 (2004); Fong et al., J. Bacteriol. 185:6400-6408 (2003); Ibarra et al., Nature 420:186-189 (2002)) that could potentially result in one strain having superior production qualities over the others. Evolutions can be run for a period of time, typically 2-6 weeks, depending upon the rate of growth improvement attained. In general, evolutions are stopped once a stable phenotype is obtained.

Following the adaptive evolution process, the new strains are characterized again by measuring the growth rate, the substrate uptake rate, and the product/byproduct secretion rate. These results are compared to the theoretical predictions by plotting actual growth and production yields along side the production envelopes from metabolic modeling. The most successful design/evolution combinations are chosen to pursue further, and are characterized in lab-scale batch and continuous fermentations. The growth-coupled biochemical production concept behind the methods disclosed herein such as OptKnock approach should also result in the generation of genetically stable overproducers. Thus, the cultures are maintained in continuous mode for an extended period of time, for example, one month or more, to evaluate long-term stability. Periodic samples can be taken to ensure that yield and productivity are maintained.

Adaptive evolution is a powerful technique that can be used to increase growth rates of mutant or engineered microbial strains, or of wild-type strains growing under unnatural environmental conditions. It is especially useful for strains designed via methods such as OptKnock, which results in growth-coupled product formation. Therefore, evolution toward optimal growing strains will indirectly optimize production as well. Unique strains of E. coli K-12 MG1655 were created through gene knockouts and adaptive evolution. (Fong and Palsson, Nat. Genet. 36:1056-1058 (2004)). In this work, all adaptive evolutionary cultures were maintained in prolonged exponential growth by serial passage of batch cultures into fresh medium before the stationary phase was reached, thus rendering growth rate as the primary selection pressure. Knockout strains were constructed and evolved on minimal medium supplemented with different carbon substrates (four for each knockout strain). Evolution cultures were carried out in duplicate or triplicate, giving a total of 50 evolution knockout strains. The evolution cultures were maintained in exponential growth until a stable growth rate was reached. The computational predictions were accurate (within 10%) at predicting the post-evolution growth rate of the knockout strains in 38 out of the 50 cases examined. Furthermore, a combination of OptKnock design with adaptive evolution has led to improved lactic acid production strains. (Fong et al., Biotechnol. Bioeng. 91:643-648 (2005)). Similar methods can be applied to the strains disclosed herein and applied to various host strains.

There are a number of developed technologies for carrying out adaptive evolution. Exemplary methods are disclosed herein. In some embodiments, optimization of a non-naturally occurring organism of the present invention includes utilizing adaptive evolution techniques to increase butadiene or 2,4-pentadienoate production and/or stability of the producing strain.

Serial culture involves repetitive transfer of a small volume of grown culture to a much larger vessel containing fresh growth medium. When the cultured organisms have grown to saturation in the new vessel, the process is repeated. This method has been used to achieve the longest demonstrations of sustained culture in the literature (Lenski and Travisano, Proc. Nat. Acad Sci. USA 91:6808-6814 (1994)) in experiments which clearly demonstrated consistent improvement in reproductive rate over a period of years. Typically, transfer of cultures is usually performed during exponential phase, so each day the transfer volume is precisely calculated to maintain exponential growth through the next 24 hour period. Manual serial dilution is inexpensive and easy to parallelize.

In continuous culture the growth of cells in a chemostat represents an extreme case of dilution in which a very high function of the cell population remains. As a culture grows and becomes saturated, a small proportion of the grown culture is replaced with fresh media, allowing the culture to continually grow at close to its maximum population size. Chemostats have been used to demonstrate short periods of rapid improvement in reproductive rate (Dykhuizen, Methods Enzymol. 613-631(1993)). The potential usefulness of these devices was recognized, but traditional chemostats were unable to sustain long periods of selection for increased reproduction rate, due to the unintended selection of dilution-resistant (static) variants. These variants are able to resist dilution by adhering to the surface of the chemostat, and by doing so, outcompete less adherent individuals, including those that have higher reproductive rates, thus obviating the intended purpose of the device (Chao and Ramsdell, J. Gen. Microbiol 20:132-138 (1985)). One possible way to overcome this drawback is the implementation of a device with two growth chambers, which periodically undergo transient phases of sterilization, as described previously (Marliere and Mutzel, U.S. Pat. No. 6,686,194).

Evolugator™ is a continuous culture device developed by Evolugate, LLC (Gainesville, Fla.) and exhibits significant time and effort savings over traditional evolution techniques (de Crecy et al., Appl. Microbiol. Biotechnol. 77:489-496 (2007)). The cells are maintained in prolonged exponential growth by the serial passage of batch cultures into fresh medium before the stationary phase is attained. By automating optical density measurement and liquid handling, the Evolugator™ can perform serial transfer at high rates using large culture volumes, thus approaching the efficiency of a chemostat in evolution of cell fitness. For example, a mutant of Acinetobacter sp ADP1 deficient in a component of the translation apparatus, and having severely hampered growth, was evolved in 200 generations to 80% of the wild-type growth rate. However, in contrast to the chemostat which maintains cells in a single vessel, the machine operates by moving from one “reactor” to the next in subdivided regions of a spool of tubing, thus eliminating any selection for wall-growth. The transfer volume is adjustable, and normally set to about 50%. A drawback to this device is that it is large and costly, thus running large numbers of evolutions in parallel is not practical. Furthermore, gas addition is not well regulated, and strict anaerobic conditions are not maintained with the current device configuration. Nevertheless, this is an alternative method to adaptively evolve a production strain.

As disclosed herein, a nucleic acid encoding a desired activity of a butadiene or 2,4-pentadienoate pathway can be introduced into a host organism. In some cases, it can be desirable to modify an activity of a butadiene or 2,4-pentadienoate pathway enzyme or protein to increase production of butadiene or 2,4-pentadienoate. For example, known mutations that increase the activity of a protein or enzyme can be introduced into an encoding nucleic acid molecule. Additionally, optimization methods can be applied to increase the activity of an enzyme or protein and/or decrease an inhibitory activity, for example, decrease the activity of a negative regulator.

One such optimization method is directed evolution. Directed evolution is a powerful approach that involves the introduction of mutations targeted to a specific gene in order to improve and/or alter the properties of an enzyme. Improved and/or altered enzymes can be identified through the development and implementation of sensitive high-throughput screening assays that allow the automated screening of many enzyme variants (for example, >10⁴). Iterative rounds of mutagenesis and screening typically are performed to afford an enzyme with optimized properties. Computational algorithms that can help to identify areas of the gene for mutagenesis also have been developed and can significantly reduce the number of enzyme variants that need to be generated and screened. Numerous directed evolution technologies have been developed (for reviews, see Hibbert et al., Biomol. Eng 22:11-19 (2005); Huisman and Lalonde, In Biocatalysis in the pharmaceutical and biotechnology industries pgs. 717-742 (2007), Patel (ed.), CRC Press; Otten and Quax. Biomol. Eng 22:1-9 (2005); and Sen et al., Appl Biochem. Biotechnol 143:212-223 (2007)) to be effective at creating diverse variant libraries, and these methods have been successfully applied to the improvement of a wide range of properties across many enzyme classes. Enzyme characteristics that have been improved and/or altered by directed evolution technologies include, for example: selectivity/specificity, for conversion of non-natural substrates; temperature stability, for robust high temperature processing; pH stability, for bioprocessing under lower or higher pH conditions; substrate or product tolerance, so that high product titers can be achieved; binding (K_(m)), including broadening substrate binding to include non-natural substrates; inhibition (K_(i)), to remove inhibition by products, substrates, or key intermediates; activity (kcat), to increases enzymatic reaction rates to achieve desired flux; expression levels, to increase protein yields and overall pathway flux; oxygen stability, for operation of air sensitive enzymes under aerobic conditions; and anaerobic activity, for operation of an aerobic enzyme in the absence of oxygen.

A number of exemplary methods have been developed for the mutagenesis and diversification of genes to target desired properties of specific enzymes. Such methods are well known to those skilled in the art. Any of these can be used to alter and/or optimize the activity of a butadiene or 2,4-pentadionate pathway enzyme or protein. Such methods include, but are not limited to EpPCR, which introduces random point mutations by reducing the fidelity of DNA polymerase in PCR reactions (Pritchard et al., J Theor. Biol. 234:497-509 (2005)); Error-prone Rolling Circle Amplification (epRCA), which is similar to epPCR except a whole circular plasmid is used as the template and random 6-mers with exonuclease resistant thiophosphate linkages on the last 2 nucleotides are used to amplify the plasmid followed by transformation into cells in which the plasmid is re-circularized at tandem repeats (Fujii et al., Nucleic Acids Res. 32:e145 (2004); and Fujii et al., Nat. Protoc. 1:2493-2497 (2006)); DNA or Family Shuffling, which typically involves digestion of two or more variant genes with nucleases such as Dnase I or EndoV to generate a pool of random fragments that are reassembled by cycles of annealing and extension in the presence of DNA polymerase to create a library of chimeric genes (Stemmer, Proc Natl Acad Sci USA 91:10747-10751(1994); and Stemmer, Nature 370:389-391(1994)); Staggered Extension (StEP), which entails template priming followed by repeated cycles of 2 step PCR with denaturation and very short duration of annealing/extension (as short as 5 sec) (Zhao et al., Nat. Biotechnol. 16:258-261(1998)); Random Priming Recombination (RPR), in which random sequence primers are used to generate many short DNA fragments complementary to different segments of the template (Shao et al., Nucleic Acids Res 26:681-683 (1998)).

Additional methods include Heteroduplex Recombination, in which linearized plasmid DNA is used to form heteroduplexes that are repaired by mismatch repair (Volkov et al, Nucleic Acids Res. 27:e18 (1999); and Volkov et al., Methods Enzymol. 328:456-463 (2000)); Random Chimeragenesis on Transient Templates (RACHITT), which employs Dnase I fragmentation and size fractionation of single stranded DNA (ssDNA) (Coco et al., Nat. Biotechnol. 19:354-359 (2001)); Recombined Extension on Truncated templates (RETT), which entails template switching of unidirectionally growing strands from primers in the presence of unidirectional ssDNA fragments used as a pool of templates (Lee et al., J. Molec. Catalysis 26:119-129 (2003)); Degenerate Oligonucleotide Gene Shuffling (DOGS), in which degenerate primers are used to control recombination between molecules; (Bergquist and Gibbs, Methods Mol. Biol 352:191-204 (2007); Bergquist et al., Biomol. Eng 22:63-72 (2005); Gibbs et al., Gene 271:13-20 (2001)); Incremental Truncation for the Creation of Hybrid Enzymes (ITCHY), which creates a combinatorial library with 1 base pair deletions of a gene or gene fragment of interest (Ostermeier et al., Proc. Natl. Acad. Sci. USA 96:3562-3567 (1999); and Ostermeier et al., Nat. Biotechnol. 17:1205-1209 (1999)); Thio-Incremental Truncation for the Creation of Hybrid Enzymes (THIO-ITCHY), which is similar to ITCHY except that phosphothioate dNTPs are used to generate truncations (Lutz et al., Nucleic Acids Res 29:E16 (2001)); SCRATCHY, which combines two methods for recombining genes, ITCHY and DNA shuffling (Lutz et al., Proc. Natl. Acad. Sci. USA 98:11248-11253 (2001)); Random Drift Mutagenesis (RNDM), in which mutations made via epPCR are followed by screening/selection for those retaining usable activity (Bergquist et al., Biomol. Eng. 22:63-72 (2005)); Sequence Saturation Mutagenesis (SeSaM), a random mutagenesis method that generates a pool of random length fragments using random incorporation of a phosphothioate nucleotide and cleavage, which is used as a template to extend in the presence of “universal” bases such as inosine, and replication of an inosine-containing complement gives random base incorporation and, consequently, mutagenesis (Wong et al., Biotechnol. J. 3:74-82 (2008); Wong et al., Nucleic Acids Res. 32:e26 (2004); and Wong et al., Anal. Biochem. 341:187-189 (2005)); Synthetic Shuffling, which uses overlapping oligonucleotides designed to encode “all genetic diversity in targets” and allows a very high diversity for the shuffled progeny (Ness et al., Nat. Biotechnol. 20:1251-1255 (2002)); Nucleotide Exchange and Excision Technology NexT, which exploits a combination of dUTP incorporation followed by treatment with uracil DNA glycosylase and then piperidine to perform endpoint DNA fragmentation (Muller et al., Nucleic Acids Res. 33:e117 (2005)).

Further methods include Sequence Homology-Independent Protein Recombination (SHIPREC), in which a linker is used to facilitate fusion between two distantly related or unrelated genes, and a range of chimeras is generated between the two genes, resulting in libraries of single-crossover hybrids (Sieber et al., Nat. Biotechnol. 19:456-460 (2001)); Gene Site Saturation Mutagenesis™ (GSSM™), in which the starting materials include a supercoiled double stranded DNA (dsDNA) plasmid containing an insert and two primers which are degenerate at the desired site of mutations (Kretz et al., Methods Enzymol. 388:3-11(2004)); Combinatorial Cassette Mutagenesis (CCM), which involves the use of short oligonucleotide cassettes to replace limited regions with a large number of possible amino acid sequence alterations (Reidhaar-Olson et al. Methods Enzymol. 208:564-586 (1991); and Reidhaar-Olson et al. Science 241:53-57 (1988)); Combinatorial Multiple Cassette Mutagenesis (CMCM), which is essentially similar to CCM and uses epPCR at high mutation rate to identify hot spots and hot regions and then extension by CMCM to cover a defined region of protein sequence space (Reetz et al., Angew. Chem. Int. Ed Engl. 40:3589-3591(2001)); the Mutator Strains technique, in which conditional ts mutator plasmids, utilizing the mutD5 gene, which encodes a mutant subunit of DNA polymerase III, to allow increases of 20 to 4000-X in random and natural mutation frequency during selection and block accumulation of deleterious mutations when selection is not required (Selifonova et al., Appl. Environ. Microbiol. 67:3645-3649 (2001)); Low et al., J. Mol. Biol. 260:359-3680 (1996)).

Additional exemplary methods include Look-Through Mutagenesis (LTM), which is a multidimensional mutagenesis method that assesses and optimizes combinatorial mutations of selected amino acids (Rajpal et al., Proc. Nat. Acad Sci. USA 102:8466-8471(2005)); Gene Reassembly, which is a DNA shuffling method that can be applied to multiple genes at one time or to create a large library of chimeras (multiple mutations) of a single gene (Tunable GeneReassembly™ (TGR™) Technology supplied by Verenium Corporation), in Silico Protein Design Automation (PDA), which is an optimization algorithm that anchors the structurally defined protein backbone possessing a particular fold, and searches sequence space for amino acid substitutions that can stabilize the fold and overall protein energetics, and generally works most effectively on proteins with known three-dimensional structures (Hayes et al., Proc. Nat. Acad Sci. USA 99:15926-15931(2002)); and Iterative Saturation Mutagenesis (ISM), which involves using knowledge of structure/function to choose a likely site for enzyme improvement, performing saturation mutagenesis at chosen site using a mutagenesis method such as Stratagene QuikChange (Stratagene; San Diego Calif.), screening/selecting for desired properties, and, using improved clone(s), starting over at another site and continue repeating until a desired activity is achieved (Reetz et al., Nat. Protoc. 2:891-903 (2007); and Reetz et al., Angew. Chem. Int. Ed Engl. 45:7745-7751(2006)).

Any of the aforementioned methods for mutagenesis can be used alone or in any combination. Additionally, any one or combination of the directed evolution methods can be used in conjunction with adaptive evolution techniques, as described herein.

Example I Production of Butadiene or 2,4-pentadienoate via 4-hydroxy-2-oxovalerate

Pathways to butadiene and 2,4-pentadienoate are shown in FIG. 1. These pathways start with intermediates of central metabolism, pyruvate and acetyl-CoA. Acetyl-CoA is reduced to acetaldehyde by an acylating acetaldehyde dehydrogenase followed by an aldolase combining pyruvate and acetaldehyde to form 4-hydroxy-2-oxovalerate (Steps A and B). In several organisms, as described in more detail below, a bifunctional enzyme can carry out these two steps and the toxic intermediate, acetaldehyde, is not released but is rather channeled within the enzyme. 4-hydroxy 2-oxovalerate can then dehydrated to form 2-oxopentenoate (Step C). Subsequently, this metabolite can be reduced to form 2-hydroxypentenoate (Step D). 2-hydroxypentenoate can be dehydrated to form 2,4-pentadienoate that can be further decaboxylated to form butadiene (Steps E and F respectively).

Alternatively, 2-oxopentenoate can be activated to form 2-oxopentenoyl-CoA either by a ligase or a CoA transferase (Steps G and H) that can then be reduced to form 2-hydroxypentenoyl-CoA (Step I). The latter can be dehydrated to form 2,4-pentadienoyl-CoA (Step L) which is converted to 2,4-pentadienoate either by a CoA hydrolase or a CoA tranferase (Step M or N). 2-Hydroxypentenoate can also be activated to form 2-hydroxypentenoyl-CoA as shown in Steps J and K, which can then be converted to 2,4-pentadienoyl-CoA as discussed above. In all the pathway combinations outlined herein, the activation of the acid intermediate to its CoA form can also be enabled by a CoA synthetase. This enzyme requires 2 ATP equivalents for achieving this activation.

This set of pathways via 2,4-pentadienoate affords a theoretical maximum yield of 1 mol butadiene per mole glucose (0.3 g/g) as shown below: C₆H₁₂O₆=C₄H₆+H₂+2CO₂+2H₂O

The pathway has a net excess redox of 1 mole/mole butadiene produced. The energetics of the pathway are quite favorable and the pathway through steps A-F has a net excess of 2 moles ATP/mole butadiene produced. If any other permutations of the pathway that activate the acid intermediates to CoA via a ligase or a transferase are used along with a CoA hydrolase, one ATP is required. This still keeps the pathway energetically favorable and brings the net ATP to 1 mole per mole butadiene produced. However, if a CoA transferase is used in Steps G or J along with a CoA transferase in Step N, the net ATP produced by the pathway still stays at 2 moles ATP/mole glucose.

One advantage of having a butadiene or 2, 4-pentadienoate producing pathway that generates ATP is producing butadiene or 2, 4-pentadienoate anaerobically. Anaerobic processes can be desirable due to the risk of explosion when oxygen is mixed with butadiene in a fermenter. Moreover, the presence of oxygen can be undesired because of its potential to cause polymerization of butadiene or 2, 4-pentadienoate. Anaerobic production can be obtained by coproduction of succinate or other byproducts with butadiene as described previously (see, e.g., WO/2014/063156A3, WO/2014/063156A2, WO/2014/055649A1, WO/2013/192183A1). However, this can cause carbon from the substrate to be lost to other products and result in reduction of the theoretical yield of butadiene or 2, 4-pentadienoate. A more preferred ananerobic process for butadiene or 2, 4-pentadienoate production is where butadiede or 2, 4-pentadienoate is produced either solely or with hydrogen such that no carbon is lost to other byproducts. For example, the pathways shown in FIG. 1 afford a maximum yield of 1 mole butadiene or 2,4-pentadienoate per mole glucose as shown below: C₆H₁₂O₆=C₄H₆+H₂+2CO₂+2H₂O

In this scenario, an excess of reducing equivalents is generated by the pathway. Since the pathway itself generates ATP, it is not required to donate the excess electrons to oxygen for oxidative phosphorylation and generation of ATP. Instead the reducing equivalent can be used for the formation of hydrogen via hydrogenases. Exemplary enzymes for these are described herein (Example XI). Further, the pathways shown in FIG. 1 proceed via acetyl-CoA and pyruvate and are amenable to carbon savings via the use of phospoketolase-dependent Acetyl-CoA synthesis pathway (Example VI). This will allow the theoretical yield of the pathway to be improved to 1.09 mole/mole as shown below and depicted in detail in FIG. 5: C₆H₁₂O₆=1.091C₄H₆+1.636CO₂+2.727H₂O

Step A, FIG. 1: Acetaldehyde Dehydrogenase

The reduction of acetyl-CoA to acetaldehyde can be catalyzed by NAD(P)+-dependent acetaldehyde dehydrogenase (EC 1.2.1.10). Acylating acetaldehyde dehydrogenases of E. coli are encoded by adhE and mhpF (Ferrandez et al, J. Bacteriol 179:2573-81(1997)). The Pseudomonas sp. CF600 enzyme, encoded by dmpF, participates in meta-cleavage pathways and forms a complex with 4-hydroxy-2-oxovalerate aldolase (Shingler et al, J Bacteriol 174:711-24 (1992)). BphJ, a nonphosphorylating acylating aldehyde dehydrogenase, catalyzes the conversion of aldehydes to form acyl-coenzyme A in the presence of NAD(+) and coenzyme A (CoA) (Baker et al., Biochemistry, 2012 Jun. 5; 51(22):4558-67. Epub 2012 May 21). Solventogenic organisms such as Clostridium acetobutylicum encode bifunctional enzymes with alcohol dehydrogenase and acetaldehyde dehydrogenase activities. The bifunctional C. acetobutylicum enzymes are encoded by bdhI and adhE2 (Walter, et al., J. Bacteriol. 174:7149-7158 (1992); Fontaine et al., J. Bacteriol. 184:821-830 (2002)). Yet another candidate for acylating acetaldehyde dehydrogenase is the ald gene from Clostridium beiyerinckii (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999). This gene is very similar to the eutE acetaldehyde dehydrogenase genes of Salmonella typhimurium and E. coli (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999).

Protein GenBank ID GI Number Organism adhE NP_415757.1 16129202 Escherichia coli mhpF NP_414885.1 16128336 Escherichia coli dmpF CAA43226.1 45683 Pseudomonas sp. CF600 adhE2 AAK09379.1 12958626 Clostridium acetobutylicum bdh I NP_349892.1 15896543 Clostridium acetobutylicum Ald AAT66436 49473535 Clostridium beijerinckii eutE NP_416950 16130380 Escherichia coli eutE AAA80209 687645 Salmonella typhimurium bphJ CAA54035.1 520923 Burkholderia xenovorans LB400

Other acyl-CoA dehydrogenases that reduce an acyl-CoA to its corresponding aldehyde include fatty acyl-CoA reductase (EC 1.2.1.42, 1.2.1.50), succinyl-CoA reductase (EC 1.2.1.76), acetyl-CoA reductase, butyryl-CoA reductase and propionyl-CoA reductase (EC 1.2.1.3). Aldehyde forming acyl-CoA reductase enzymes with demonstrated activity on acyl-CoA, 3-hydroxyacyl-CoA and 3-oxoacyl-CoA substrates are known in the literature. Several acyl-CoA reductase enzymes are active on 3-hydroxyacyl-CoA substrates. For example, some butyryl-CoA reductases from Clostridial organisms, are active on 3-hydroxybutyryl-CoA and propionyl-CoA reductase of L. reuteri is active on 3-hydroxypropionyl-CoA. An enzyme for converting 3-oxoacyl-CoA substrates to their corresponding aldehydes is malonyl-CoA reductase. Enzymes in this class can be refined using evolution or enzyme engineering methods known in the art to have activity on enoyl-CoA substrates.

Exemplary fatty acyl-CoA reductases enzymes are encoded by acr1 of Acinetobacter calcoaceticus (Reiser, Journal of Bacteriology 179:2969-2975 (1997)) and Acinetobacter sp. M-1 (Ishige et al., Appl. Environ. Microbiol. 68:1192-1195 (2002)). Two gene products from Mycobacterium tuberculosis accept longer chain fatty acyl-CoA substrates of length C16-C18 (Harminder Singh, U. Central Fla. (2007)). Yet another fatty acyl-CoA reductase is LuxC of Photobacterium phosphoreum (Lee et al, Biochim Biohys Acta 1388:215-22 (1997)). Enzymes with succinyl-CoA reductase activity are encoded by sucD of Clostridium kluyveri (Sohling, J. Bacteriol. 178:871-880 (1996)) and sucD of P. gingivalis (Takahashi, J. Bacteriol 182:4704-4710 (2000)). Additional succinyl-CoA reductase enzymes participate in the 3-hydroxypropionate/4-hydroxybutyrate cycle of thermophilic archaea including Metallosphaera sedula (Berg et al., Science 318:1782-1786 (2007)) and Thermoproteus neutrophilus (Ramos-Vera et al., J. Bacteriol, 191:4286-4297 (2009)). The M. sedula enzyme, encoded by Msed_0709, is strictly NADPH-dependent and also has malonyl-CoA reductase activity. The T. neutrophilus enzyme is active with both NADPH and NADH. The enzyme acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by bphG, is yet another as it has been demonstrated to oxidize and acylate acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and formaldehyde (Powlowski, J. Bacteriol. 175:377-385 (1993)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxidize the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya, J. Gen. Appl. Microbiol. 18:43-55 (1972); and Koo et al., Biotechnol Lett. 27:505-510 (2005)). Butyraldehyde dehydrogenase catalyzes a similar reaction, conversion of butyryl-CoA to butyraldehyde, in solventogenic organisms such as Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci Biotechnol Biochem., 71:58-68 (2007)). Exemplary propionyl-CoA reductase enzymes include pduP of Salmonella typhimurium LT2 (Leal, Arch. Microbiol. 180:353-361(2003)) and eutE from E. coli (Skraly, WO Patent No. 2004/024876). The propionyl-CoA reductase of Salmonella typhimurium LT2, which naturally converts propionyl-CoA to propionaldehyde, also catalyzes the reduction of 5-hydroxyvaleryl-CoA to 5-hydroxypentanal (WO 2010/068953A2). The propionaldehyde dehydrogenase of Lactobacillus reuteri, PduP, has a broad substrate range that includes butyraldehyde, valeraldehyde and 3-hydroxypropionaldehyde (Luo et al, Appl Microbiol Biotech, 89: 697-703 (2011)). Additionally, some acyl-ACP reductase enzymes such as the orf1594 gene product of Synechococcus elongatus PCC7942 also exhibit aldehyde-forming acyl-CoA reductase activity (Schirmer et al, Science, 329: 559-62 (2010)).

sProtein GenBank ID GI Number Organism acr1 YP_047869.1 50086359 Acinetobacter calcoaceticus acr1 AAC45217 1684886 Acinetobacter baylyi acr1 BAB85476.1 18857901 Acinetobacter sp. Strain M-1 Rv1543 NP_216059.1 15608681 Mycobacterium tuberculosis Rv3391 NP_217908.1 15610527 Mycobacterium tuberculosis LUXC AAT00788.1 46561111 Photobacterium phosphoreum MSED 0709 YP_001190808.1 146303492 Metallosphaera sedula Tneu_0421 ACB39369.1 170934108 Thermoproteus neutrophilus sucD P38947.1 172046062 Clostridium kluyveri sucD NP_904963.1 34540484 Porphyromonas gingivalis bphG BAA03892.1 425213 Pseudomonas sp adhE AAV66076.1 55818563 Leuconostoc mesenteroides bld AAP42563.1 31075383 Clostridium saccharoperbutylacetonicum pduP NP_460996 16765381 Salmonella typhimurium LT2 eutE NP_416950 16130380 Escherichia coli pduP CCC03595.1 337728491 Lactobacillus reuteri

Additionally, some acyl-ACP reductase enzymes such as the orf1594 gene product of Synechococcus elongatus PCC7942 also exhibit aldehyde-forming acyl-CoA reductase activity (Schirmer et al, Science, 329: 559-62 (2010)). The S. elongates PCC7942 acyl-ACP reductase is coexpressed with an aldehyde decarbonylase in an operon that appears to be conserved in a majority of cyanobacterial organisms. This enzyme, expressed in E. coli together with the aldehyde decarbonylase, conferred the ability to produce alkanes. The P. marinus AAR was also cloned into E. coli and, together with a decarbonylase, demonstrated production of alkanes (see, e.g., US Application 2011/0207203).

Gene GenBank ID GI Number Organism orf1594 YP_400611.1 81300403 Synechococcus elongatus PCC7942 PMT9312_0533 YP_397030.1 78778918 Prochlorococcus marinus MIT 9312 syc0051 d YP_170761.1 56750060 Synechococcus elongatus PCC 6301 Ava_2534 YP_323044.1 75908748 Anabaena variabilis ATCC 29413 alr5284 NP_489324.1 17232776 Nostoc sp. PCC 7120 Aazo_3370 YP_003722151.1 298491974 Nostoc azollae Cyan7425_0399 YP_002481152.1 220905841 Cyanothece sp. PCC 7425 N9414_21225 ZP_01628095.1 119508943 Nodularia spumigena CCY9414 L8106 07064 ZP_01619574.1 119485189 Lyngbya sp. PCC 8106

An additional enzyme type that converts an acyl-CoA to its corresponding aldehyde is malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde. Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archaeal bacteria (Berg, Science 318:1782-1786 (2007); and Thauer, Science 318:1732-1733 (2007)). The enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus sp. (Alber et al., J. Bacteriol. 188:8551-8559 (2006); and Hugler, J. Bacteriol. 184:2404-2410 (2002)). The enzyme is encoded by Msed_0709 in Metallosphaera sedula (Alber et al., J. Bacteriol. 188:8551-8559 (2006); and Berg, Science 318:1782-1786 (2007)). A gene encoding a malonyl-CoA reductase from Sulfolobus tokodaii was cloned and heterologously expressed in E. coli (Alber et al., J. Bacteriol 188:8551-8559 (2006). This enzyme has also been shown to catalyze the conversion of methylmalonyl-CoA to its corresponding aldehyde (WO2007141208 (2007)). Although the aldehyde dehydrogenase functionality of these enzymes is similar to the bifunctional dehydrogenase from Chloroflexus aurantiacus, there is little sequence similarity. Both malonyl-CoA reductase enzyme candidates have high sequence similarity to aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the reduction and concurrent dephosphorylation of aspartyl-4-phosphate to aspartate semialdehyde. Additional gene candidates can be found by sequence homology to proteins in other organisms including Sulfolobus solfataricus and Sulfolobus acidocaldarius and have been listed below. Yet another candidate for CoA-acylating aldehyde dehydrogenase is the ald gene from Clostridium beijerinckii (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999). This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes. This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999).

Gene GenBank ID GI Number Organism Msed_0709 YP_001190808.1 146303492 Metallosphaera sedula mcr NP_378167.1 15922498 Sulfolobus tokodaii asd-2 NP_343563.1 15898958 Sulfolobus solfataricus Saci 2370 YP_256941.1 70608071 Sulfolobus acidocaldarius

Step B, FIG. 1: 4-Hydroxy 2-Oxovalerate Aldolase

The condensation of pyruvate and acetaldehyde to 4-hydroxy-2-oxovalerate is catalyzed by 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39). This enzyme participates in pathways for the degradation of phenols, cresols and catechols. The E. coli enzyme, encoded by mhpE, is highly specific for acetaldehyde as an acceptor but accepts the alternate substrates 2-ketobutyrate or phenylpyruvate as donors (Pollard et al., Appl Environ Microbiol 64:4093-4094 (1998)). Similar enzymes are encoded by the cmtG and todH genes of Pseudomonas putida (Lau et al., Gene 146:7-13 (1994); Eaton, J. Bacteriol. 178:1351-1362 (1996)). In Pseudomonas CF600, this enzyme is part of a bifunctional aldolase-dehydrogenase heterodimer encoded by dmpFG (Manjasetty et al., Acta Crystallogr. D. Biol Crystallogr. 57:582-585 (2001)). The dehydrogenase functionality interconverts acetaldehyde and acetyl-CoA, providing the advantage of reduced cellular concentrations of acetaldehyde, toxic to some cells. It has been shown recently that substrate channeling can occur within this enzyme in the presence of NAD and residues that could play an important role in channeling acetaldehyde into the DmpF site were also identified.

Gene GenBank ID GI Number Organism mhpE AAC73455.1 1786548 Escherichia coli cmtG AAB62295.1 1263190 Pseudomonas putida todH AAA61944.1 485740 Pseudomonas putida dmpG CAA43227.1 45684 Pseudomonas sp. CF600 dmpF CAA43226.1 45683 Pseudomonas sp. CF600 bphI CAA54036.1 520924 Burkholderia xenovorans LB400

Step C, FIG. 1: 4-Hydroxy 2-Oxovalerate Dehydratase

The dehydration of 4-hydroxy-2-oxovalerate to 2-oxopentenoate is catalyzed by 4-hydroxy-2-oxovalerate hydratase (EC 4.2.1.80). 4-Hydroxy-2-oxovalerate hydratase participates in aromatic degradation pathways and is typically co-transcribed with a gene encoding an enzyme with 4-hydroxy-2-oxovalerate aldolase activity. Exemplary gene products are encoded by mhpD of E. coli (Ferrandez et al., J. Bacteriol. 179:2573-2581(1997); Pollard et al., Eur J Biochem. 251:98-106 (1998)), todG and cmtF of Pseudomonas putida (Lau et al., Gene 146:7-13 (1994); Eaton, J Bacteriol. 178:1351-1362 (1996)), cnbE of Comamonas sp. CNB-1 (Ma et al., Appl Environ Microbiol 73:4477-4483 (2007)) and mhpD of Burkholderia xenovorans (Wang et al., FEBS J272:966-974 (2005)). A closely related enzyme, 2-oxohepta-4-ene-1,7-dioate hydratase, participates in 4-hydroxyphenylacetic acid degradation, where it converts 2-oxo-hept-4-ene-1,7-dioate (OHED) to 2-oxo-4-hydroxy-hepta-1,7-dioate using magnesium as a cofactor (Burks et al., J. Am. Chem. Soc. 120: (1998)). OHED hydratase enzyme candidates have been identified and characterized in E. coli C (Roper et al., Gene 156:47-51(1995); Izumi et al., J Mol. Biol. 370:899-911(2007)) and E. coli W (Prieto et al., J Bacteriol. 178:111-120 (1996)). Sequence comparison reveals homologs in a wide range of bacteria, plants and animals. Enzymes with highly similar sequences are contained in Klebsiella pneumonia (91% identity, eval=2e-138) and Salmonella enterica (91% identity, eval=4e-138), among others.

Gene GenBank ID GI Number Organism mhpD AAC73453.2 87081722 Escherichia coli cmtF AAB62293.1 1263188 Pseudomonas putida todG AAA61942.1 485738 Pseudomonas putida cnbE YP_001967714.1 190572008 Comamonas sp. CNB-1 mhpD Q13VU0 123358582 Burkholderia xenovorans hpcG CAA57202.1 556840 Escherichia coli C hpaH CAA86044.1 757830 Escherichia coli W hpaH ABR80130.1 150958100 Klebsiella pneumonia Sari_01896 ABX21779.1 160865156 Salmonella enteric

2-(Hydroxymethyl)glutarate dehydratase is a [4Fe-4S]-containing enzyme that dehydrates 2-(hydroxymethyl)glutarate to 2-methylene-glutarate, studied for its role in nicontinate catabolism in Eubacterium barkeri (formerly Clostridium barkeri) (Alhapel et al., Proc Natl Acad Sci 103:12341-6 (2006)). Similar enzymes with high sequence homology are found in Bacteroides capillosus, Anaerotruncus colihominis, and Natranaerobius thermophilius. These enzymes are homologous to the alpha and beta subunits of [4Fe-4S]-containing bacterial serine dehydratases (e.g., E. coli enzymes encoded by tdcG, sdhB, and sdaA). An enzyme with similar functionality in E. barkeri is dimethylmaleate hydratase, a reversible Fe²⁺-dependent and oxygen-sensitive enzyme in the aconitase family that hydrates dimethylmaeate to form (2R,3S)-2,3-dimethylmalate. This enzyme is encoded by dmdAB (Alhapel et al., Proc Natl Acad Sci USA 103:12341-6 (2006); Kollmann-Koch et al., Hoppe Seylers. Z. Physiol Chem. 365:847-857 (1984)).

Protein GenBank ID GI Number Organism hmd ABC88407.1 86278275 Eubacterium barkeri BACCAP_02294 ZP_02036683.1 154498305 Bacteroides capillosus ANACOL_02527 ZP_02443222.1 167771169 Anaerotruncus colihominis NtherDRAFT 2368 ZP_02852366.1 169192667 Natranaerobius thermophilus dmdA ABC88408 86278276 Eubacterium barkeri dmdB ABC88409 86278277 Eubacterium barkeri

Step D, FIG. 1: 2-Oxopentenoate Reductase

The reduction of 2-oxopentenoate to 2-hydroxypentenoate is carried out by an alcohol dehydrogenase that reduces a ketone group. Several exemplary alcohol dehydrogenases can catalyze this transformation. Two such enzymes from E. coli are encoded by malate dehydrogenase (mdh) and lactate dehydrogenase (ldhA). In addition, lactate dehydrogenase from Ralstonia eutropha has been shown to demonstrate high activities on 2-ketoacids of various chain lengths including lactate, 2-oxobutyrate, 2-oxopentanoate and 2-oxoglutarate (Steinbuchel et al., Eur. J Biochem. 130:329-334 (1983)). Conversion of alpha-ketoadipate into alpha-hydroxyadipate is catalyzed by 2-ketoadipate reductase, an enzyme found in rat and in human placenta (Suda et al., Arch. Biochem. Biophys. 176:610-620 (1976); Suda et al., Biochem. Biophys. Res. Commun. 77:586-591(1977)). An additional candidate oxidoreductase is the mitochondrial 3-hydroxybutyrate dehydrogenase (bdh) from the human heart which has been cloned and characterized (Marks et al., J. Biol. Chem. 267:15459-15463 (1992)). Alcohol dehydrogenase enzymes of C. beijerinckii (Ismaiel et al., J. Bacteriol. 175:5097-5105 (1993)) and T. brockii (Lamed et al., Biochem. J. 195:183-190 (1981); Peretz et al., Biochemistry. 28:6549-6555 (1989)) convert acetone to isopropanol. Methyl ethyl ketone reductase catalyzes the reduction of MEK to 2-butanol. Exemplary MEK reductase enzymes can be found in Rhodococcus ruber (Kosjek et al., Biotechnol Bioeng. 86:55-62 (2004)) and Pyrococcus furiosus (van der et al., Eur. J Biochem. 268:3062-3068 (2001))

Gene GenBank ID GI Number Organism Mdh AAC76268.1 1789632 Escherichia coli ldhA NP_415898.1 16129341 Escherichia coli Ldh YP_725182.1 113866693 Ralstonia eutropha Bdh AAA58352.1 177198 Homo sapiens Adh AAA23199.2 60592974 Clostridium beijerinckii NRRL B593 Adh P14941.1 113443 Thermoanaerobacter brockii HTD4 Sadh CAD36475 21615553 Rhodococcus ruber adhA AAC25556 3288810 Pyrococcus furiosus

Step E, FIG. 1: 2-Hydroxypentenoate Dehydratase

Enzyme candidates for the dehydration of 2-hydroxypentenoate (FIG. 1, Step E) include fumarase (EC 4.2.1.2), citramalate hydratase (EC 4.2.1.34) and dimethylmaleate hydratase (EC 4.2.1.85). Fumarases naturally catalyze the reversible dehydration of malate to fumarate. Although the ability of fumarase to react with 2-hydroxypentenoate as substrates has not been described in the literature, a wealth of structural information is available for this enzyme and other researchers have successfully engineered the enzyme to alter activity, inhibition and localization (Weaver, Acta Crystallogr D Biol Crystallogr, 61:1395-1401 (2005)). E. coli has three fumarases: FumA, FumB, and FumC that are regulated by growth conditions. FumB is oxygen sensitive and only active under anaerobic conditions. FumA is active under microanaerobic conditions, and FumC is the only active enzyme in aerobic growth (Tseng et al., J. Bacteriol, 183:461-467 (2001); Woods et al., 954:14-26 (1988); Guest et al., J Gen Microbiol 131:2971-2984 (1985)). Additional enzyme candidates are found in Campylobacter jejuni (Smith et al., Int. J Biochem. Cell Biol 31:961-975 (1999)), Thermus thermophilus (Mizobata et al., Arch. Biochem. Biophys. 355:49-55 (1998)) and Rattus norvegicus (Kobayashi et al., J Biochem, 89:1923-1931(1981)). Similar enzymes with high sequence homology include fum1 from Arabidopsis thaliana and fumC from Corynebacterium glutamicum. The mmcBC fumarase from Pelotomaculum thermopropionicum is another class of fumarase with two subunits (Shimoyama et al., FEMS Microbiol Lett, 270:207-213 (2007)). Citramalate hydrolyase naturally dehydrates 2-methylmalate to mesaconate. This enzyme has been studied in Methanocaldococcus jannaschii in the context of the pyruvate pathway to 2-oxobutanoate, where it has been shown to have a broad substrate specificity (Drevland et al., J Bacteriol. 189:4391-4400 (2007)). This enzyme activity was also detected in Clostridium tetanomorphum, Morganella morganii, Citrobacter amalonaticus where it is thought to participate in glutamate degradation (Kato et al., Arch. Microbiol 168:457-463 (1997)). The M. jannaschii protein sequence does not bear significant homology to genes in these organisms. Dimethylmaleate hydratase is a reversible Fe²⁺-dependent and oxygen-sensitive enzyme in the aconitase family that hydrates dimethylmaeate to form (2R,3S)-2,3-dimethylmalate. This enzyme is encoded by dmdAB in Eubacterium barkeri (Alhapel et al., supra; Kollmann-Koch et al., Hoppe Seylers. Z. Physiol Chem. 365:847-857 (1984)).

Gene GenBank ID GI Number Organism fumA NP_416129.1 16129570 Escherichia coli fumB NP_418546.1 16131948 Escherichia coli fumC NP_416128.1 16129569 Escherichia coli fumC O69294 9789756 Campylobacter jejuni fumC P84127 75427690 Thermus thermophilus fumH P14408 120605 Rattus norvegicus fum1 P93033 39931311 Arabidopsis thaliana fumC Q8NRN8 39931596 Corynebacterium glutamicum mmcB YP_001211906 147677691 Pelotomaculum thermopropionicum mmcC YP_001211907 147677692 Pelotomaculum thermopropionicum leuD Q58673.1 3122345 Methanocaldococcus jannaschii dmdA ABC88408 86278276 Eubacterium barkeri dmdB ABC88409.1 86278277 Eubacterium barkeri

Oleate hydratases catalyze the reversible hydration of non-activated alkenes to their corresponding alcohols. These enzymes represent additional suitable candidates as suggested in WO2011076691. Oleate hydratases from Elizabethkingia meningoseptica and Streptococcus pyogenes have been characterized (WO 2008/119735). Examples include the following proteins.

Protein GenBank ID GI Number Organism OhyA ACT54545.1 254031735 Elizabethkingia meningoseptica HMPREF0841 1446 ZP_07461147.1 306827879 Streptococcus pyogenes ATCC 10782 P700755 13397 ZP_01252267.1 91215295 Psychroflexus torquis ATCC 700755 RPB 2430 YP_486046.1 86749550 Rhodopseudomonas palustris

Step F, FIG. 1: 2,4-Pentadienoate Decarboxylase

The decarboxylation reactions of 2,4-pentadienoate to butadiene (step F of FIG. 1) are catalyzed by enoic acid decarboxylase enzymes. Exemplary enzymes are sorbic acid decarboxylase, aconitate decarboxylase, 4-oxalocrotonate decarboxylase and cinnamate decarboxylase. Sorbic acid decarboxylase converts sorbic acid to 1,3-pentadiene. Sorbic acid decarboxylation by Aspergillus niger requires three genes:padA1, ohbA1, and sdrA (Plumridge et al. Fung. Genet. Bio, 47:683-692 (2010). PadA1 is annotated as a phenylacrylic acid decarboxylase, ohbA1 is a putative 4-hydroxybenzoic acid decarboxylase, and sdrA is a sorbic acid decarboxylase regulator. Additional species have also been shown to decarboxylate sorbic acid including several fungal and yeast species (Kinderlerler and Hatton, Food Addit Contam., 7(5):657-69 (1990); Casas et al., Int J Food Micro., 94(1):93-96 (2004); Pinches and Apps, Int. J Food Microbiol. 116: 182-185 (2007)). For example, Aspergillus oryzae and Neosartorya fischeri have been shown to decarboxylate sorbic acid and have close homologs to padA1, ohbA1, and sdrA.

Gene name GenBankID GI Number Organism padA1 XP_001390532.1 145235767 Aspergillus niger ohbA1 XP_001390534.1 145235771 Aspergillus niger sdrA XP_001390533.1 145235769 Aspergillus niger padA1 XP_001818651.1 169768362 Aspergillus oryzae ohbA1 XP_001818650.1 169768360 Aspergillus oryzae sdrA XP_001818649.1 169768358 Aspergillus oryzae padA1 XP_001261423.1 119482790 Neosartorya fischeri ohbA1 XP_001261424.1 119482792 Neosartorya fischeri sdrA XP_001261422.1 119482788 Neosartorya fischeri

Aconitate decarboxylase (EC 4.1.1.6) catalyzes the final step in itaconate biosynthesis in a strain of Candida and also in the filamentous fungus Aspergillus terreus (Bonnarme et al. J. Bacteriol. 177:3573-3578 (1995); Willke and Vorlop, Appl Microbiol. Biotechnol 56:289-295 (2001)). A cis-aconitate decarboxylase (CAD) (EC 4.1.16) has been purified and characterized from Aspergillus terreus (Dwiarti et al., J Biosci. Bioeng. 94(1): 29-33 (2002)). Recently, the gene has been cloned and functionally characterized (Kanamasa et al., Appl. Microbiol Biotechnol 80:223-229 (2008)) and (WO/2009/014437). Several close homologs of CAD are listed below (EP 2017344A1; WO 2009/014437 A1). The gene and protein sequence of CAD were reported previously (EP 2017344 A1; WO 2009/014437 A1), along with several close homologs listed in the table below.

Gene name GenBankID GI Number Organism CAD XP_001209273 115385453 Aspergillus terreus XP_001217495 115402837 Aspergillus terreus XP_001209946 115386810 Aspergillus terreus BAE66063 83775944 Aspergillus oryzae XP_001393934 145242722 Aspergillus niger XP_391316 46139251 Gibberella zeae XP_001389415 145230213 Aspergillus niger XP_001383451 126133853 Pichia stipitis YP_891060 118473159 Mycobacterium smegmatis NP_961187 41408351 Mycobacterium avium subsp. pratuberculosis YP_880968 118466464 Mycobacterium avium ZP_01648681 119882410 Salinispora arenicola

An additional class of decarboxylases has been characterized that catalyze the conversion of cinnamate (phenylacrylate) and substituted cinnamate derivatives to the corresponding styrene derivatives. These enzymes are common in a variety of organisms and specific genes encoding these enzymes that have been cloned and expressed in E. coli are: pad from Saccharomyces cerevisae (Clausen et al., Gene 142:107-112 (1994)), pdc from Lactobacillus plantarum (Barthelmebs et al., Appl Environ Microbiol. 67:1063-1069 (2001); Qi et al., Metab Eng 9:268-276 (2007); Rodriguez et al., J. Agric. Food Chem. 56:3068-3072 (2008)), pofK (pad) from Klebsiella oxytoca (Uchiyama et al., Biosci. Biotechnol. Biochem. 72:116-123 (2008); Hashidoko et al., Biosci. Biotech. Biochem. 58:217-218 (1994)), Pedicoccus pentosaceus (Barthelmebs et al., Appl Environ Microbiol. 67:1063-1069 (2001)), and padC from Bacillus subtilis and Bacillus pumilus (Shingler et al., J. Bacteriol., 174:711-724 (1992)). A ferulic acid decarboxylase from Pseudomonas fluorescens also has been purified and characterized (Huang et al., J. Bacteriol. 176:5912-5918 (1994)). Importantly, this class of enzymes have been shown to be stable and do not require either exogenous or internally bound co-factors, thus making these enzymes ideally suitable for biotransformations (Sariaslani, Annu. Rev. Microbiol. 61:51-69 (2007)).

Protein GenBank ID GI Number Organism pad1 AAB64980.1 1165293 Saccharomyces cerevisae ohbA1 BAG32379.1 188496963 Saccharomyces cerevisiae pdc AAC45282.1 1762616 Lactobacillus plantarum pad BAF65031.1 149941608 Klebsiella oxytoca padC NP_391320.1 16080493 Bacillus subtilis pad YP_804027.1 116492292 Pedicoccus pentosaceus pad CAC18719.1 11691810 Bacillus pumilus

4-Oxalocronate decarboxylase catalyzes the decarboxylation of 4-oxalocrotonate to 2-oxopentanoate. This enzyme has been isolated from numerous organisms and characterized. The decarboxylase typically functions in a complex with vinylpyruvate hydratase. Genes encoding this enzyme include dmpH and dmpE in Pseudomonas sp. (strain 600) (Shingler et al., J. Bacteriol., 174:711-724 (1992)), xylII and xylIII from Pseudomonas putida (Kato et al., Arch. Microbiol 168:457-463 (1997); Stanley et al., Biochemistry 39:3514 (2000); Lian et al., J. Am. Chem. Soc. 116:10403-10411(1994)) and Reut B5691 and Reut B5692 from Ralstonia eutropha JMP134 (Hughes et al., J Bacteriol, 158:79-83 (1984)). The genes encoding the enzyme from Pseudomonas sp. (strain 600) have been cloned and expressed in E. coli (Shingler et al., Bacteriol. 174:711-724 (1992)). The 4-oxalocrotonate decarboxylase encoded by xylI in Pseudomonas putida functions in a complex with vinylpyruvate hydratase. A recombinant form of this enzyme devoid of the hydratase activity and retaining wild type decarboxylase activity has been characterized (Stanley et al., Biochem. 39:718-26 (2000)). A similar enzyme is found in Ralstonia pickettii (formerly Pseudomonas pickettii) (Kukor et al., J. Bacteriol. 173:4587-94 (1991)).

Gene GenBank GI Number Organism dmpH CAA43228.1 45685 Pseudomonas sp. CF600 dmpE CAA43225.1 45682 Pseudomonas sp. CF600 xylII YP_709328.1 111116444 Pseudomonas putida xylIII YP_709353.1 111116469 Pseudomonas putida Reut_B5691 YP_299880.1 73539513 Ralstonia eutroha JMP134 Reut_B5692 YP_299881.1 73539514 Ralstonia eutropha JMP134 xylI P49155.1 1351446 Pseudomonas putida tbuI YP_002983475.1 241665116 Ralstonia pickettii nbaG BAC65309.1 28971626 Pseudomonas fluorescens KU-7

Numerous characterized enzymes decarboxylate amino acids and similar compounds, including aspartate decarboxylase, lysine decarboxylase and omithine decarboxylase. Aspartate decarboxylase (EC 4.1.1.11) decarboxylates aspartate to form beta-alanine. This enzyme participates in pantothenate biosynthesis and is encoded by gene panD in Escherichia coli (Dusch et al., Appl. Environ. Microbiol 65:1530-1539 (1999); Ramjee et al., Biochem. J 323 (Pt 3):661-669 (1997); Merkel et al., FEMS Microbiol Lett. 143:247-252 (1996); Schmitzberger et al., EMBO J 22:6193-6204 (2003)). The enzymes from Mycobacterium tuberculosis (Chopm et al., Protein Expr. Purif 25:533-540 (2002)) and Corynebacterium glutanicum (Dusch et al., Appl. Environ. Microbiol 65:1530-1539 (1999)) have been expressed and characterized in E. coli.

Protein GenBank ID GI Number Organism panD P0A790 67470411 Escherichia coli K12 panD Q9X4N0 18203593 Corynebacterium glutanicum panD P65660.1 54041701 Mycobacterium tuberculosis

Lysine decarboxylase (EC 4.1.1.18) catalyzes the decarboxylation of lysine to cadaverine. Two isozymes of this enzyme are encoded in the E. coli genome by genes cadA and ldcC. CadA is involved in acid resistance and is subject to positive regulation by the cadC gene product (Lemonnier et al., Microbiology 144 (Pt 3):751-760 (1998)). CadC accepts hydroxylysine and S-aminoethylcysteine as alternate substrates, and 2-aminopimelate and 6-aminocaproate act as competitive inhibitors to this enzyme (Sabo et al., Biochemistry 13:662-670 (1974)). The constitutively expressed ldc gene product is less active than CadA (Lemonnier and Lane, Microbiology 144 (Pt 3):751-760 (1998)). A lysine decarboxylase analogous to CadA was recently identified in Vibrio parahaemolyticus (Tanaka et al., J Appl Microbiol 104:1283-1293 (2008)). The lysine decarboxylase from Selenomonas ruminantium, encoded by ldc, bears sequence similarity to eukaryotic omithine decarboxylases, and accepts both L-lysine and L-omithine as substrates (Takatsuka et al., Biosci. Biotechnol Biochem. 63:1843-1846 (1999)). Active site residues were identified and engineered to alter the substrate specificity of the enzyme (Takatsuka et al., J. Bacteriol. 182:6732-6741(2000)). Several omithine decarboxylase enzymes (EC 4.1.1.17) also exhibit activity on lysine and other similar compounds. Such enzymes are found in Nicotiana glutinosa (Lee et al., Biochem. J360:657-665 (2001)), Lactobacillus sp. 30a (Guirard et al., J Biol. Chem. 255:5960-5964 (1980)) and Vibrio vulnificus (Lee et al., J Biol. Chem. 282:27115-27125 (2007)). The enzymes from Lactobacillus sp. 30a (Momany et al., J Mol. Biol. 252:643-655 (1995)) and V. vulnificus have been crystallized. The V. vulnificus enzyme efficiently catalyzes lysine decarboxylation and the residues involved in substrate specificity have been elucidated (Lee et al., J Biol. Chem. 282:27115-27125 (2007)). A similar enzyme has been characterized in Trichomonas vaginalis. (Yarlett et al., Biochem. J293 (Pt 2):487-493 (1993)).

Protein GenBank ID GI Number Organism cadA AAA23536.1 145458 Escherichia coli IdcC AAC73297.1 1786384 Escherichia coli Ldc O50657.1 13124043 Selenomonas ruminantium cadA AB124819.1 44886078 Vibrio parahaemolyticus AF323910.1:1..1299 AAG45222.1 12007488 Nicotiana glutinosa odc1 P43099.2 1169251 Lactobacillus sp. 30a VV2_1235 NP_763142.1 27367615 Vibrio vulnificus Steps G and J, FIG. 1: 2-Oxopentenoate Ligase and 2-Hydroxypentenoate Ligase

ADP and AMP-forming CoA ligases (6.2.1) with broad substrate specificities have been described in the literature. The ADP-forming acetyl-CoA synthetase (ACD, EC 6.2.1.13) from Archaeoglobus fulgidus, encoded by AF1211, was shown to operate on a variety of linear and branched-chain substrates including isobutyrate, isopentanoate, and fumarate (Musfeldt et al., J. Bacteriol. 184:636-644 (2002)). A second reversible ACD in Archaeoglobus fulgidus, encoded by AF1983, was also indicated to have a broad substrate range (Musfeldt et al., supra). The enzyme from Haloarcula marismortui, annotated as a succinyl-CoA synthetase, accepts propionate, butyrate, and branched-chain acids (isovalerate and isobutyrate) as substrates, and was shown to operate in the forward and reverse directions (Brasen et al., Arch. Microbiol 182:277-287 (2004)). The ACD encoded by PAE3250 from hyperthermophilic crenarchaeon Pyrobaculum aerophilum showed the broadest substrate range of all characterized ACDs, reacting with acetyl-CoA, isobutyryl-CoA (preferred substrate) and phenylacetyl-CoA (Brasen and Schonheit, Arch. Microbiol 182:277-287 (2004)). Directed evolution or engineering can be used to modify this enzyme to operate at the physiological temperature of the host organism. The enzymes from A. fulgidus, H. marismortui and P. aerophilum have all been cloned, functionally expressed, and characterized in E. coli (Brasen and Schonheit, Arch. Microbiol 182:277-287 (2004); Musfeldt and Schonheit, J. Bacteriol. 184:636-644 (2002)). An additional enzyme is encoded by sucCD in E. coli, which naturally catalyzes the formation of succinyl-CoA from succinate with the concomitant consumption of one ATP, a reaction which is reversible in vivo (Buck et al., Biochemistry 24:6245-6252 (1985)). The acyl CoA ligase from Pseudomonas putida has been indicated to work on several aliphatic substrates including acetic, propionic, butyric, valeric, hexanoic, heptanoic, and octanoic acids and on aromatic compounds such as phenylacetic and phenoxyacetic acids (Femandez-Valverde et al., Appl. Environ. Microbiol. 59:1149-1154 (1993)). A related enzyme, malonyl CoA synthetase (6.3.4.9) from Rhizobium leguminosarum could convert several diacids, namely, ethyl-, propyl-, allyl-, isopropyl-, dimethyl-, cyclopropyl-, cyclopropylmethylene-, cyclobutyl-, and benzyl-malonate into their corresponding monothioesters (Pohl et al., J. Am. Chem. Soc. 123:5822-5823 (2001)). Recently, a CoA dependent acetyl-CoA ligase was also identified in Propionibacterium acidipropionici ATCC 4875 (Parizzi et al., BMC Genomics. 2012; 13: 562). This enzyme is distinct from the AMP-dependent acetyl-CoA synthetase and is instead related to the ADP-forming succinyl-CoA synthetase complex (SCSC). Genes releted to the SCSC (α and β subunits) complex were also found in Propionibacterium acnes KPA171202 and Microlunatus phophovorus NM-1.

The acylation of acetate to acetyl-CoA is catalyzed by enzymes with acetyl-CoA synthetase activity. Two enzymes that catalyze this reaction are AMP-forming acetyl-CoA synthetase (EC 6.2.1.1) and ADP-forming acetyl-CoA synthetase (EC 6.2.1.13). AMP-forming acetyl-CoA synthetase (ACS) is the predominant enzyme for activation of acetate to acetyl-CoA. Exemplary ACS enzymes are found in E. coli (Brown et al., J. Gen. Microbiol 102:327-336 (1977)), Rastonia eutropha (Priefert et. al., J. Bacteriol 174:6590-6599(1992)), Methanothermobacter thermautotrophicus (Ingram-Smith et al., Archaea. 2:95-107 (2007)), Salmonella enterica (Gulick et al., Biochemistry 42:2866-2873 (2003)) and Saccharomyces cerevisiae (Jogl et al., Biochemistry, 43:1425-1431(2004)).

Methylmalonyl-CoA synthetase from Rhodopseudomonas palustris (MatB) converts methylmalonate and malonate to methyhnalonyl-CoA and malonyl-CoA, respectively. Structure-based mutagenesis of this enzyme improved CoA synthetase activity with the alternate substrates ethylmalonate and butylmalonate (Crosby et al, AEM, in press (2012)).

GenBank Gene Accession No. GI No. Organism AF1211 NP_070039.1 11498810 Archaeoglobus fulgidus AF1983 NP_070807.1 11499565 Archaeoglobus fulgidus Scs YP_135572.1 55377722 Haloarcula marismortui PAE3250 NP_560604.1 18313937 Pyrobaculum aerophilum str. IM2 sucC NP_415256.1 16128703 Escherichia coli sucD AAC73823.1 1786949 Escherichia coli paaF AAC24333.2 22711873 Pseudomonas putida matB AAC83455.1 3982573 Rhizobium leguminosarum Acs AAC77039.1 1790505 Escherichia coli acoE AAA21945.1 141890 Ralstonia eutropha acs1 ABC87079.1 86169671 Methanothermobacter thermautotrophicus acs1 AAL23099.1 16422835 Salmonella enterica ACS1 Q01574.2 257050994 Saccharomyces cerevisiae LSC1 NP_014785 6324716 Saccharomyces cerevisiae LSC2 NP_011760 6321683 Saccharomyces cerevisiae bioW NP_390902.2 50812281 Bacillus subtilis bioW CAA10043.1 3850837 Pseudomonas mendocina bioW P22822.1 115012 Bacillus sphaericus Phl CAJ15517.1 77019264 Penicillium chrysogenum phlB ABS19624.1 152002983 Penicillium chrysogenum paaF AAC24333.2 22711873 Pseudomonas putida PACID_02150 YP_006979420.1 410864809 Propionibacterium acidipropionici ATCC 4875 PPA1754 AAT83483.1 50840816 Propionibacterium acnes KPA171202 PPA1755 AAT83484.1 50840817 Propionibacterium acnes KPA171202 Subunit alpha YP_004571669.1 336116902 Microlunatus phosphovorus NM-1 Subunit beta YP_004571668.1 336116901 Microlunatus phosphovorus NM-1 AACS NP_084486.1 21313520 Mus musculus AACS NP_076417.2 31982927 Homo sapiens

4HrB-CoA synthetase catalyzes the ATP-dependent conversion of 4-hydroxybutyrate to 4-hydroxybutyryl-CoA. AMP-forming 4-HB-CoA synthetase enzymes are found in organisms that assimilate carbon via the dicarboxylate/hydroxybutyrate cycle or the 3-hydroxypropionate/4-hydroxybutyrate cycle. Enzymes with this activity have been characterized in Thermoproteus neutrophilus and Metallosphaera sedula (Ramos-Vera et al, J. Bacteriol 192:532-940 (2010); Berg et al, Science 318:1782-6 (2007)). Others can be inferred by sequence homology.

Protein GenBank ID GI Number Organism Tneu_0420 ACB39368.1 170934107 Thermoproteus neutrophilus Caur_0002 YP_001633649.1 163845605 Chloroflexus aurantiacus J-10-fl Cagg_3790 YP_002465062 219850629 Chloroflexus aggregans DSM 9485 Acs YP_003431745 288817398 Hydrogenobacter thermophilus TK-6 Pisl_0250 YP_929773.1 119871766 Pyrobaculum islandicum DSM 4184 Msed 1422 ABP95580.1 145702438 Metallosphaera sedula

Step I, FIG. 1: 2-Oxopentenoyl-CoA Reductase

The reduction of 2-oxopentenoyl CoA to 2-hydroxypentanoyl-CoA can be accomplished by 3-oxoacyl-CoA reductase enzymes (EC 1.1.1.35) that typically convert 3-oxoacyl-CoA molecules into 3-hydroxyacyl-CoA molecules and are often involved in fatty acid beta-oxidation or phenylacetate catabolism. For example, subunits of two fatty acid oxidation complexes in E. coli, encoded by fadB and fadJ, function as 3-hydroxyacyl-CoA dehydrogenases (Binstock et al., Methods Enzymol. 71 Pt C:403-411(1981)). Given the proximity in E. coli of paaH to other genes in the phenylacetate degradation operon (Nogales et al., Microbiology, 153:357-365 (2007)) and the fact that paaH mutants cannot grow on phenylacetate (Ismail et al., Eur. J Biochem. 270:3047-3054 (2003)), it is expected that the E. coli paaH gene also encodes a 3-hydroxyacyl-CoA dehydrogenase. Additional 3-oxoacyl-CoA enzymes include the gene products of phaC in Pseudomonas putida (Olivera et al., Proc. Natl. Acad Sci USA 95:6419-6424 (1998)) and paaC in Pseudomonas fluorescens (Di et al., Arch. Microbiol 188:117-125 (2007)). These enzymes catalyze the reversible oxidation of 3-hydroxyadipyl-CoA to 3-oxoadipyl-CoA during the catabolism of phenylacetate or styrene.

Acetoacetyl-CoA reductase participates in the acetyl-CoA fermentation pathway to butyrate in several species of Clostridia and has been studied in detail (Jones et al., Microbiol Rev. 50:484-524 (1986)). The enzyme from Clostridium acetobutylicum, encoded by hbd, has been cloned and functionally expressed in E. coli (Youngleson et al., J. Bacteriol. 171:6800-6807 (1989)). Yet other genes demonstrated to reduce acetoacetyl-CoA to 3-hydroxybutyryl-CoA are phbB from Zoogloea ramigera (Ploux et al., Eur. J Biochem. 174:177-182 (1988)) and phaB from Rhodobacter sphaeroides (Alber et al., Mol. Microbiol 61:297-309 (2006)). The former gene is NADPH-dependent, its nucleotide sequence has been determined (Peoples et al., Mol. Microbiol 3:349-357 (1989)) and the gene has been expressed in E. coli. Substrate specificity studies on the gene led to the conclusion that it could accept 3-oxopropionyl-CoA as a substrate besides acetoacetyl-CoA (Ploux et al., Eur. J Biochem. 174:177-182 (1988)). Additional genes include phaB in Paracoccus denitrifcans, Hbd1 (C-terminal domain) and Hbd2 (N-terminal domain) in Clostridium kluyveri (Hillmer and Gottschalk, Biochim. Biophys. Acta 3334:12-23 (1974)) and HSD17B10 in Bos taurus (Wakil et al., J Biol. Chem. 207:631-638 (1954)). The enzyme from Paracoccus denitrifcans has been functionally expressed and characterized in E. coli (Yabutani et al., FEMS Microbiol Lett. 133:85-90 (1995)). A number of similar enzymes have been found in other species of Clostridia and in Metallosphaera sedula (Berg et al., Science. 318:1782-1786 (2007)). The enzyme from Candida tropicalis is a component of the peroxisomal fatty acid beta-oxidation multifunctional enzyme type 2 (MFE-2). The dehydrogenase B domain of this protein is catalytically active on acetoacetyl-CoA. The domain has been functionally expressed in E. coli, a crystal structure is available, and the catalytic mechanism is well-understood (Ylianttila et al., Biochem Biophys Res Commun 324:25-30 (2004); Ylianttila et al., J Mol Biol 358:1286-1295 (2006)). 3-Hydroxyacyl-CoA dehydrogenases that accept longer acyl-CoA substrates (eg. EC 1.1.1.35) are typically involved in beta-oxidation. An example is HSD17B10 in Bos taurus (WAKIL et al., J Biol. Chem. 207:631-638 (1954)). phbB from Cupriavidus necatar codes for a 3-hydroxyvaleryl-CoA dehydrogenase activity.

Protein GENBANK ID GI NUMBER ORGANISM fadB P21177.2 119811 Escherichia coli fadJ P77399.1 3334437 Escherichia coli paaH NP_415913.1 16129356 Escherichia coli Hbd2 EDK34807.1 146348271 Clostridium kluyveri Hbd1 EDK32512.1 146345976 Clostridium kluyveri phaC NP_745425.1 26990000 Pseudomonas putida paaC ABF82235.1 106636095 Pseudomonas fluorescens HSD17B10 O02691.3 3183024 Bos Taurus phbB P23238.1 130017 Zoogloea ramigera phaB YP_353825.1 77464321 Rhodobacter sphaeroides phaB BAA08358 675524 Paracoccus denitrificans phbB AEI82198.1 338171145 Cupriavidus necator Hbd NP_349314.1 15895965 Clostridium acetobutylicum Hbd AAM14586.1 20162442 Clostridium beijerinckii Msed_1423 YP_001191505 146304189 Metallosphaera sedula Msed 0399 YP_001190500 146303184 Metallosphaera sedula Msed 0389 YP_001190490 146303174 Metallosphaera sedula Msed_1993 YP_001192057 146304741 Metallosphaera sedula Fox2 Q02207 399508 Candida tropicalis HSD17B10 O02691.3 3183024 Bos Taurus

Other exemplary enzymes that can carry this reaction are 2-hydroxyacid dehydrogenases. Such an enzyme, characterized from the halophilic archaeon Haloferax mediterranei catalyses a reversible stereospecific reduction of 2-ketocarboxylic acids into the corresponding D-2-hydroxycarboxylic acids. The enzyme is strictly NAD-dependent and prefers substrates with a main chain of 3-4 carbons (pyruvate and 2-oxobutanoate). Activity with 4-methyl-2-oxopentanoate is 10-fold lower. Two such enzymes from E. coli are encoded by malate dehydrogenase (mch) and lactate dehydrogenase (ldhA). In addition, lactate dehydrogenase from Ralstonia eutropha has been shown to demonstate high activities on 2-ketoacids of various chain lengths including lactate, 2-oxobutyrate, 2-oxopentanoate and 2-oxoglutarate (Steinbuchel et al., Eur. J Biochem. 130:329-334 (1983)). Conversion of alpha-ketoadipate into alpha-hydroxyadipate can be catalyzed by 2-ketoadipate reductase, an enzyme reported to be found in rat and in human placenta (Suda et al., Arch. Biochem. Biophys. 176:610-620 (1976); Suda et al., Biochem. Biophys. Res. Commun. 77:586-591(1977)). An additional oxidoreductase is the mitochondrial 3-hydroxybutyrate dehydrogenase (bdh) from the human heart which has been cloned and characterized (Marks et al., J Biol. Chem. 267:15459-15463 (1992)). Alcohol dehydrogenase enzymes of C. beijerinckii (Ismaiel et al., J. Bacteriol. 175:5097-5105 (1993)) and T. brockii (Lamed et al., Biochem. J. 195:183-190 (1981); Peretz et al., Biochemistry. 28:6549-6555 (1989)) convert acetone to isopropanol. Methyl ethyl ketone reductase catalyzes the reduction of MEK to 2-butanol. Exemplary MEK reductase enzymes can be found in Rhodococcus ruber (Kosjek et al., Biotechnol Bioeng. 86:55-62 (2004)) and Pyrococcus furiosus (van der et al., Eur. J Biochem. 268:3062-3068 (2001)).

GenBank Gene Accession No. GI No. Organism mdh AAC76268.1 1789632 Escherichia coli ldhA NP_415898.1 16129341 Escherichia coli ldh YP_725182.1 113866693 Ralstonia eutropha bdh AAA58352.1 177198 Homo sapiens adh AAA23199.2 60592974 Clostridium beijerinckii NRRL B593 adh P14941.1 113443 Thermoanaerobacter brockii HTD4 sadh CAD36475 21615553 Rhodococcus ruber adhA AAC25556 3288810 Pyrococcus furiosus BM92_14160 AHZ23715.1 631806019 Haloferax mediterranei ATCC 33500

Step M, FIG. 1: 2,4-Pentadienoyl-CoA Hydrolase

CoA hydrolysis of 2,4-pentadienoyl CoA can be catalyzed by CoA hydrolases or thioesterases in the EC class 3.1.2. Several CoA hydrolases with broad substrate ranges are suitable enzymes for hydrolyzing these intermediates. For example, the enzyme encoded by acot12 from Rattus norvegicus brain (Robinson et al., Biochem. Biophys. Res. Commun. 71:959-965 (1976)) can react with butyryl-CoA, hexanoyl-CoA and malonyl-CoA. The human dicarboxylic acid thioesterase, encoded by acot8, exhibits activity on glutaryl-CoA, adipyl-CoA, suberyl-CoA, sebacyl-CoA, and dodecanedioyl-CoA (Westin et al., J Biol. Chem. 280:38125-38132 (2005)). The closest E. coli homolog to this enzyme, tesB, can also hydrolyze a range of CoA thiolesters (Naggert et al., J Biol Chem 266:11044-11050(1991)). A similar enzyme has also been characterized in the rat liver (Deana R., Biochem Int 26:767-773 (1992)). Additional enzymes with hydrolase activity in E. coli include ybgC, paaI, yciA, and ybdB (Kuznetsova, et al., FEMS Microbiol Rev, 2005, 29(2):263-279; Song et al., J Biol Chem, 2006, 281(16):11028-38). Though its sequence has not been reported, the enzyme from the mitochondrion of the pea leaf has a broad substrate specificity, with demonstrated activity on acetyl-CoA, propionyl-CoA, butyryl-CoA, palmitoyl-CoA, oleoyl-CoA, succinyl-CoA, and crotonyl-CoA (Zeiher et al., Plant. Physiol. 94:20-27 (1990)) The acetyl-CoA hydrolase, ACH1, from S. cerevisiae represents another candidate hydrolase (Buu et al., J. Biol. Chem. 278:17203-17209 (2003)).

GenBank Gene name Accession # GI# Organism acot12 NP_570103.1 18543355 Rattus norvegicus tesB NP_414986 16128437 Escherichia coli acot8 CAA15502 3191970 Homo sapiens acot8 NP_570112 51036669 Rattus norvegicus tesA NP_415027 16128478 Escherichia coli ybgC NP_415264 16128711 Escherichia coli paaI NP_415914 16129357 Escherichia coli ybdB NP_415129 16128580 Escherichia coli ACH1 NP_009538 6319456 Saccharomyces cerevisiae yciA NP_415769.1 16129214 Escherichia coli

Yet another candidate hydrolase is the glutaconate CoA-transferase from Acidaminococcus fermentans. This enzyme was transformed by site-directed mutagenesis into an acyl-CoA hydrolase with activity on glutaryl-CoA, acetyl-CoA and 3-butenoyl-CoA (Mack et al., FEBS. Lett. 405:209-212 (1997)). This suggests that the enzymes encoding succinyl-CoA:3-ketoacid-CoA transferases and acetoacetyl-CoA:acetyl-CoA transferases may also serve as candidates for this reaction step but would require certain mutations to change their function.

GenBank Gene name Accession # GI# Organism gctA CAA57199 559392 Acidaminococcus fermentans gctB CAA57200 559393 Acidaminococcus fermentans

Additional hydrolase enzymes include 3-hydroxyisobutyryl-CoA hydrolase which has been described to efficiently catalyze the conversion of 3-hydroxyisobutyryl-CoA to 3-hydroxyisobutyrate during valine degradation (Shimomuia et al., J Biol Chem. 269:14248-14253 (1994)). Genes encoding this enzyme include hibch of Rattus norvegicus (Shimomura et al., Methods Enzymol. 324:229-240 (2000)) and Homo sapiens (Shimomura et al., supra). Similar gene candidates can also be identified by sequence homology, including hibch of Saccharomyces cerevisiae and BC_2292 of Bacillus cereus.

GenBank Gene name Accession # GI# Organism hibch Q5XIE6.2 146324906 Rattus norvegicus hibch Q6NVY1.2 146324905 Homo sapiens hibch P28817.2 2506374 Saccharomyces cerevisiae BC_2292 AP09256 29895975 Bacillus cereus

Methylmalonyl-CoA is converted to methylmalonate by methylmalonyl-CoA hydrolase (EC 3.1.2.7). This enzyme, isolated from Rattus norvegicus liver, is also active on malonyl-CoA and propionyl-CoA as alternative substrates (Kovachy et al., J Biol. Chem., 258: 11415-11421(1983)).

Steps H, K and N, FIG. 1: 2-Oxopentenoate:Acetyl CoA Transferase, 2-Hydroxypentenoate:Acetyl-CoA CoA Transferase, 2,4-Pentadienoyl-CoA:Acetyl CoA CoA Transferase

Several transformations require a CoA transferase to activate carboxylic acids to their corresponding acyl-CoA derivatives. CoA transferase enzymes have been described in the open literature and represent suitable candidates for these steps. These are described below.

The gene products of cat1, cat2, and cat3 of Clostridium kluyveri have been shown to exhibit succinyl-CoA, 4-hydoxybutyryl-CoA, and butyryl-CoA transferase activity, respectively (Seedorf et al., Proc. Natl. Acad Sci USA 105:2128-2133 (2008); Sohling et al., J. Bacteriol. 178:871-880 (1996)). Similar CoA transferase activities are also present in Trichomonas vaginalis, Trypanosoma brucei, Clostridium aminobutyricum and Porphyromonas gingivalis (Riviere et al., J. Biol. Chem. 279:45337-45346 (2004); van Grinsven et al., J Biol. Chem. 283:1411-1418 (2008)).

Protein GenBank ID GI Number Organism cat1 P38946.1 729048 Clostridium kluyveri cat2 P38942.2 172046066 Clostridium kluyveri cat3 EDK35586.1 146349050 Clostridium kluyveri TVAG_395550 XP_001330176 123975034 Trichomonas vaginalis G3 Tb11.02.0290 XP_828352 71754875 Trypanosoma brucei cat2 CAB60036.1 6249316 Clostridium aminobutyricum cat2 NP_906037.1 34541558 Porphyromonas gingivalis W83

A fatty acyl-CoA transferase that utilizes acetyl-CoA as the CoA donor is acetoacetyl-CoA transferase, encoded by the E. coli atoA (alpha subunit) and atoD (beta subunit) genes (Korolev et al., Acta Crystallogr. D. Biol. Crystallogr. 58:2116-2121(2002); Vanderwinkel et al., 33:902-908 (1968)). This enzyme has a broad substrate range on substrates of chain length C3-C6 (Sramek et al., Arch Biochem Biophys 171:14-26 (1975)) and has been shown to transfer the CoA moiety to acetate from a variety of branched and linear 3-oxo and acyl-CoA substrates, including isobutyrate (Matthies et al., Appl Environ Microbiol 58:1435-1439 (1992)), valerate (Vanderwinkel et al., Biochem. Biophys. Res. Commun. 33:902-908 (1968)) and butanoate (Vanderwinkel et al., Biochem. Biophys. Res. Commun. 33:902-908 (1968)). This enzyme is induced at the transcriptional level by acetoacetate, so modification of regulatory control may be necessary for engineering this enzyme into a pathway (Pauli et al., Eur. J Biochem. 29:553-562 (1972)). Similar enzymes exist in Corynebacterium glutamicum ATCC 13032 (Duncan et al., Appl Environ Microbiol, 68:5186-5190 (2002)), Clostridium acetobutylicum (Cary et al., Appl Environ Microbiol 56:1576-1583 (1990); Wiesenbom et al., Appl Environ Microbiol 55:323-329 (1989)), and Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci. Biotechnol Biochem. 71:58-68 (2007)).

Gene GI # Accession No. Organism atoA 2492994 P76459.1 Escherichia coli atoD 2492990 P76458.1 Escherichia coli actA 62391407 YP_226809.1 Corynebacterium glutamicum cg0592 62389399 YP_224801.1 Corynebacterium glutamicum ctfA 15004866 NP_149326.1 Clostridium acetobutylicum ctfB 15004867 NP_149327.1 Clostridium acetobutylicum ctfA 31075384 AAP42564.1 Clostridium saccharoperbutylacetonicum ctfB 31075385 AAP42565.1 Clostridium saccharoperbutylacetonicum

Step L, FIG. 1: 2-hydroxypentenoyl-CoA Dehydratase

The dehydration of 2-hydroxypentenoyl-CoA can be catalyzed by a special class of oxygen-sensitive enzymes that dehydrate 2-hydroxyacyl-CoA derivatives by a radical-mechanism (Buckel and Golding, Annu. Rev. Microbiol. 60:2749 (2006); Buckel et al., Curr. Opin. Chem. Biol. 8:462-467 (2004); Buckel et al., Biol. Chem. 386:951-959 (2005); Kim et al., FEBS J. 272:550-561(2005); Kim et al., FEMS Microbiol. Rev. 28:455-468 (2004); Zhang et al., Microbiology 145 (Pt 9):2323-2334 (1999)). One example of such an enzyme is the lactyl-CoA dehydratase from Clostridium propionicum, which catalyzes the dehydration of lactoyl-CoA to form acryloyl-CoA (Kuchta and Abeles, J Biol. Chem. 260:13181-13189 (1985); Hofimeister and Buckel, Eur. J Biochem. 206:547-552 (1992)). An additional example is 2-hydroxyglutaryl-CoA dehydratase encoded by hgdABC from Acidaminococcus fermentans (Mueller and Buckel, Eur. J Biochem. 230:698-704 (1995); Schweiger et al., Eur. J. Biochem. 169:441-448 (1987)). Purification of the dehydratase from A. fermentans yielded two components, A and D. Component A (HgdC) acts as an activator or initiator of dehydration. Component D is the actual dehydratase and is encoded by HgdAB. Variations of this enzyme have been found in Clostridum symbiosum and Fusobacterium nucleatum. Component A, the activator, from A. fermentans is active with the actual dehydrates (component D) from C. symbiosum and is reported to have a specific activity of 60 per second, as compared to 10 per second with the component D from A. fermentans. Yet another example is the 2-hydroxyisocaproyl-CoA dehydratase from Clostridium difficile catalyzed by hadBC and activated by hadI (Darley et al., FEBS J. 272:550-61(2005)). The sequence of the complete C. propionicium lactoyl-CoA dehydratase is not yet listed in publicly available databases. However, the sequence of the beta-subunit corresponds to the GenBank accession number AJ276553 (Selmer et al, Eur J Biochem, 269:372-80 (2002)). The dehydratase from Clostridium sporogens that dehydrates phenyllactyl-CoA to cinnamoyl-CoA is also a potential candidate for this step. This enzyme is composed of three subunits, one of which is a CoA transferase. The first step comprises of a CoA transfer from cinnamoyl-CoA to phenyllactate leading to the formation of phenyllactyl-CoA and cinnamate. The product cinnamate is released. The dehydratase then converts phenyllactyl-CoA into cinnamoyl-CoA. FdA is the CoA transferase and FldBC are related to the alpha and beta subunits of the dehydratase, component D, from A. fermentans.

Gene GenBank Accession No. GI No. Organism hgdA P11569 296439332 Acidaminococcus fermentans hgdB P11570 296439333 Acidaminococcus fermentans hgdC P11568 2506909 Acidaminococcus ftrmentans hgdA AAD31676.1 4883832 Clostridum symbiosum hgdB AAD31677.1 4883833 Clostridum symbiosum hgdC AAD31675.1 4883831 Clostridum symbiosum hgdA EDK88042.1 148322792 Fusobacterium nucleatum hgdB EDK88043.1 148322793 Fusobacterium nucleatum hgdC EDK88041.1 148322791 Fusobacterium nucleatum FldB Q93AL9.1 75406928 Clostridium sporogens FldC Q93AL8.1 75406927 Clostridium sporogens hadB YP_001086863 126697966 Clostridium difficile hadC YP_001086864 126697967 Clostridium difficile hadI YP_001086862 126697965 Clostridium difficile lcdB AJ276553 7242547 Clostridium propionicum

Another dehydratase that can potentially conduct such a biotransformation is the enoyl-CoA hydratase (4.2.1.17) of Pseudomonas putida, encoded by ech that catalyzes the conversion of 3-hydroxybutyryl-CoA to crotonyl-CoA (Roberts et al., Arch. Microbiol 117:99-108 (1978)). This transformation is also catalyzed by the crt gene product of Clostridium acetobutylicum, the crt1 gene product of C. kluyveri, and other clostridial organisms Atsumi et al., Metab Eng 10:305-311(2008); Boynton et al., J. Bacteriol. 178:3015-3024 (1996); Hillmer et al., FEBS Lett. 21:351-354 (1972)). Additional enoyl-CoA hydratase candidates are phaA and phaB, of P. putida, and paaA and paaB from P. fluorescens (Olivera et al., Proc. Natl. Acad. Sci USA 95:6419-6424 (1998)). The gene product of pimF in Rhodopseudomonas palustris is predicted to encode an enoyl-CoA hydratase that participates in pimeloyl-CoA degradation (Harrison et al., Microbiology 151:727-736 (2005)). Lastly, a number of Escherichia coli genes have been shown to demonstrate enoyl-CoA hydratase functionality including maoC (Park et al., J. Bacteriol. 185:5391-5397 (2003)), paaF (Ismail et al., Eur. J Biochem. 270:3047-3054 (2003); Park et al., Appl. Biochem. Biotechnol 113-116:335-346 (2004); Park et al., Biotechnol Bioeng 86:681-686 (2004)) and paaG (Ismail et al., Eur. J Biochem. 270:3047-3054 (2003); Park and Lee, Appl. Biochem. Biotechnol 113-116:335-346 (2004); Park and Yup, Biotechnol Bioeng 86:681-686 (2004)).

GenBank Gene Accession No. GI No. Organism ech NP_745498.1 26990073 Pseudomonas putida crt NP_349318.1 15895969 Clostridium acetobutylicum crt1 YP_001393856 153953091 Clostridium kluyveri phaA NP_745427.1 26990002 Pseudomonas putida KT2440 phaB NP_745426.1 26990001 Pseudomonas putida KT2440 paaA ABF82233.1 106636093 Pseudomonas fluorescens paaB ABF82234.1 106636094 Pseudomonas fluorescens maoC NP_415905.1 16129348 Escherichia coli paaF NP_415911.1 16129354 Escherichia coli paaG NP_415912.1 16129355 Escherichia coli

Alternatively, the E. coli gene products of fadA and fadB encode a multienzyme complex involved in fatty acid oxidation that exhibits enoyl-CoA hydratase activity (Yang et al., Biochemistry 30:6788-6795 (1991); Yang, J Bacteriol. 173:7405-7406 (1991); Nakahigashi et al., Nucleic Acids Res. 18:4937(1990)). Knocking out a negative regulator encoded by fadR can be utilized to activate the fadB gene product (Sato et al., J Biosci. Bioeng 103:3844 (2007)). The fadI and fadJ genes encode similar functions and are naturally expressed under anaerobic conditions (Campbell et al., Mol. Microbiol 47:793-805 (2003)).

Protein GenBank ID GI Number Organism fadA YP_026272.1 49176430 Escherichia coli fadB NP_418288.1 16131692 Escherichia coli fadI NP_416844.1 16130275 Escherichia coli fadJ NP_416843.1 16130274 Escherichia coli fadR NP_415705.1 16129150 Escherichia coli

Example II Production of Butadiene or 2,4-Pentadienoate Via 3-Oxoglutaryl-CoA

Pathways to butadiene or 2,4-pentadienoate production as depicted in FIG. 2 starts with combining acetyl-CoA and malonyl-CoA via a thiolase (Step B). Acetyl-CoA can be carboxylated to form malonyl-CoA via an acetyl-CoA carboxylase (Step A). The product of the thiolase transformation in Step B is 3-oxoglutaryl-CoA. This can be reduced to form 3-hydroxyglutaryl-CoA(Step C). The latter can then be reduced to form 3-hydroxy 5-oxopentanoate and then 3,5-dihydroxypentanoate via an aldehyde forming 3-hydroxyglutaryl-CoA reductase and 3-hydroxy-5-oxopentanoate reductase respectively (Steps D and E). Alternatively, 3-hydroxyglutaryl-CoA can be reduced by an alcohol-forming 3-hydroxyglutaryl-CoA reductase to form 3,5-dihydroxypentanoate (Step F). Steps G and H in the pathway are two dehydration steps that dehydrate 3,5-dihydroxypentanoate to 5-hydroxy pent-2-enoate and to pent-2,4-dienoate respectively. This is eventually decarboxylated to form butadiene (Step I). 3-Hydroxy-5-oxopentanoate can also be formed from 3-oxoglutaryl-CoA via phosphate-3-hydroxyglutaryl transferase and 3-hydroxy-5-oxopentanoate synthase as shown in Steps R and S.

Alternatively, 3,5-dihydroxypentanoate can be activated to form 3,5-dihydroxypentanoyl-CoA (Step J or K), which is then dehydrated to form 5-hydroxypent-2-enoyl-CoA (Step L). Further dehydration of the latter leads to the formation of penta-2,4-dienoyl-CoA (Step 0). This metabolite is then hydrolyzed to form 2,4-pentadienoate (Step P or Q). A CoA transferase can also be used for this effect. 2,4-pentadienoate is then decarboxylated to form butadiene (Step I). The intermediate 5-hydroxypent-2-enoate can also be converted to form 5-hydroxypent-2-enoyl-CoA either by a CoA ligase or a CoA transferase (Step M or N). This CoA intermediate is then dehydrated to form 2,4-pentadienoyl-CoA as shown in Step O.

These pathways afford a maximum theoretical yield of 1 mol butadiene/mol glucose with a net excess of one mole NAD(P)H per mole butadiene formed. These pathway can also make up to one mole of ATP per mole of butadiene formed. Some combinations of these pathways will proceed through Steps A through I. Certain combinations of these pathways will be ATP neutral. For example, when a CoA ligase is used to activate one of the acid intermediates in the pathway and then CoA hydrolysis is used to form 2,4-pentadienoate, ATP production is neutral. The ATP-generating pathways also therefore provide an opportunity to produce butadiene anaerobically with coproduction of hydrogen. As described for the pathways described in FIG. 1, this set of pathways also allows for accomplishing a yield increase in butadiene with the use of a phosphoketolase-dependent acetyl-CoA synthesis pathway (See Example VI below).

Step a, FIG. 2: Acetyl-CoA Carboxylase

Acetyl-CoA carboxylase (EC 6.4.1.2) catalyzes the ATP-dependent carboxylation of acetyl-CoA to malonyl-CoA. This enzyme is biotin dependent and is the first reaction of fatty acid biosynthesis initiation in several organisms. Exemplary enzymes are encoded by accABCD of E. coli (Davis et al, J Biol Chem 275:28593-8 (2000)), ACC1 of Saccharomyces cerevisiae and homologs (Sumper et al, Methods Enzym 71:34-7 (1981)). The mitochondrial acetyl-CoA carboxylase of S. cerevisiae is encoded by HFA1. Acetyl-CoA carboxylase holoenzyme formation requires attachment of biotin by a biotin:apoprotein ligase such as BPL1 of S. cerevisiae. These and additional ACC enzymes are listed in the table below.

Protein GenBank ID GI Number Organism ACC1 CAA96294.1 1302498 Saccharomyces cerevisiae KELA0F06072g XP_455355.1 50310667 Kluyveromyces lactis ACC1 XP_718624.1 68474502 Candida albicans YALI0C11407p XP_501721.1 50548503 Yarrowia lipolytica ANI 1 1724104 XP_001395476.1 145246454 Aspergillus niger accA AAC73296.1 1786382 Escherichia coli accB AAC76287.1 1789653 Escherichia coli accC AAC76288.1 1789654 Escherichia coli accD AAC75376.1 1788655 Escherichia coli accA CAD08690.1 16501513 Salmonella enterica accB CAD07894.1 16504441 Salmonella enterica accC CAD07895.1 16504442 Salmonella enterica accD CAD07598.1 16503590 Salmonella enterica HFA1 NP_013934.1 6323863 Saccharomyces cerevisiae BPL1 NP_010140.1 6320060 Saccharomyces cerevisiae YMR207C NP_013934.1 6323863 Saccharomyces cerevisiae YNR016C NP_014413.1 6324343 Saccharomyces cerevisiae YGR037C NP_011551.1 6321474 Saccharomyces cerevisiae YKL182W NP_012739.1 6322666 Saccharomyces cerevisiae YPL231W NP_015093.1 6325025 Saccharomyces cerevisiae accA ZP_00618306.1 69288468 Kineococcus radiotolerans accB ZP_00618387.1 69288621 Kineococcus radiotolerans accC ZP_00618040.1/ 69287824/ Kineococcus radiotolerans ZP_00618387.1 69288621 accD ZP_00618306.1 69288468 Kineococcus radiotolerans

Malonyl-CoA can also be produced from malonate, produced either intracellularly or from exogenously fed malonate. Organisms are known to convert malonate into malonyl-CoA either by a synthetase or via a CoA transferase. Additionally, the ability to uptake malonate can be conferred upon an organism by introducing a malonate transporter as described in Chen and Tan (Appl Biochem Biotechnol. 2013 September; 171(1):44-62). In this paper, a malonate transporter encoded by mae1 was cloned from Schizosaccharomyces pombe into Saccharomyces cerevesiae.

Malonyl-CoA synthetase converts malonate into malonyl-CoA while converting ATP into AMP. This enzyme was first discovered in bacteroids, Bradyrhizobium japonicum, of soyabean nodules (Kim and Chae, 1990). Free malonate is known to occur in legumes and its levels increase under symbiotic conditions. The enzyme has been purified from B. japonicum and from Rhizobium leguminosarium bv trifolii (kim et al., 1993). In the latter, a mat operon is described that comprises of a malonate carrier (matC), a malonyl-CoA synthetase (matB), a malonyl-CoA decarboxylase (matA) and the regulator of the operon, matR.

Protein GenBank ID GI Number Organism Mae1 CAC37422.1 13810233 Schizosaccharomyces pombe matA AAC83456.1 3982574 Rhizobium leguminosarium matB AAC83455.1 3982573 Rhizobium leguminosarium matC AAC83457.1 3982575 Rhizobium leguminosarium

Step B: FIG. 2: Malonyl-CoA:Acetyl-CoA Acyltransferase

Beta-ketothiolase enzymes catalyzing the formation of beta-ketovalerate from acetyl-CoA and propionyl-CoA are suitable candidates for catalyzing the condensation of acetyl-CoA and malonyl-CoA. Zoogloea ramigera possesses two ketothiolases that can form 3-ketovaleryl-CoA from propionyl-CoA and acetyl-CoA and R. eutropha has a beta-oxidation ketothiolase that is also capable of catalyzing this transformation (Grays et al., U.S. Pat. No. 5,958,745 (1999)). The sequences of these genes or their translated proteins have not been reported, but several candidates in R. eutropha, Z. ramigera, or other organisms can be identified based on sequence homology to bktB from R. eutropha. These include:

Protein GenBank ID GI Number Organism phaA YP_725941.1 113867452 Ralstonia eutropha h16_A1713 YP_726205.1 113867716 Ralstonia eutropha pcaF YP_728366.1 116694155 Ralstonia eutropha h16 B1369 YP_840888.1 116695312 Ralstonia eutropha h16 A0170 YP_724690.1 113866201 Ralstonia eutropha h16_A0462 YP_724980.1 113866491 Ralstonia eutropha h16_A1528 YP_726028.1 113867539 Ralstonia eutropha h16 B0381 YP_728545.1 116694334 Ralstonia eutropha h16 B0662 YP_728824.1 116694613 Ralstonia eutropha h16_B0759 YP_728921.1 116694710 Ralstonia eutropha h16_B0668 YP_728830.1 116694619 Ralstonia eutropha h16_A1720 YP_726212.1 113867723 Ralstonia eutropha h16 A1887 YP_726356.1 113867867 Ralstonia eutropha phbA P07097.4 135759 Zoogloea ramigera bktB YP_002005382.1 194289475 Cupriavidus taiwanensis Rmet_1362 YP_583514.1 94310304 Ralstonia metallidurans Bphy_0975 YP_001857210.1 186475740 Burkholderia phymatum

Another suitable candidate is 3-oxoadipyl-CoA thiolase (EC 2.3.1.174), which converts beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA, and is a key enzyme of the beta-ketoadipate pathway for aromatic compound degradation. The enzyme is widespread in soil bacteria and fungi including Pseudomonas putida (Harwood et al., J Bacteriol. 176:6479-6488 (1994)) and Acinetobacter calcoaceticus (Doten et al., J. Bacteriol. 169:3168-3174(1987)). The gene products encoded by pcaF in Pseudomonas strain B13 (Kaschabek et al., J. Bacteriol. 184:207-215 (2002)), phaD in Pseudomonas putida U (Olivera et al., Proc. Natl. Acad Sci USA 95:6419-6424 (1998)), paaE in Pseudomonas fluorescens ST (Di et al., Arch. Microbiol 188:117-125 (2007)), and paaJ from E. coli (Nogales et al., Microbiology 153:357-365 (2007)) also catalyze this transformation. Several beta-ketothiolases exhibit significant and selective activities in the oxoadipyl-CoA forming direction including bkt from Pseudomonas putida, pcaF and bkt from Pseudomonas aeruginosa PAO1, bkt from Burkholderia ambifaria AMNMD, paaJ from E. coli, and phaD from P. putida.

GenBank Gene name GI# Accession # Organism paaJ 16129358 NP_415915.1 Escherichia coli pcaF 17736947 AAL02407 Pseudomonas knackmussii (B13) phaD 3253200 AAC24332.1 Pseudomonas putida pcaF 506695 AAA85138.1 Pseudomonas putida pcaF 141777 AAC37148.1 Acinetobacter calcoaceticus paaE 106636097 ABF82237.1 Pseudomonas fluorescens bkt 115360515 YP_777652.1 Burkholderia ambifaria AMMD bkt 9949744 AAG06977.1 Pseudomonas aeruginosa PAO1 pcaF 9946065 AAG03617.1 Pseudomonas aeruginosa PAO1

3-Oxopimeloyl-CoA thiolase catalyzes the condensation of glutaryl-CoA and acetyl-CoA into 3-oxopimeloyl-CoA (EC 2.3.1.16). An enzyme catalyzing this transformation is encoded by genes bktB and bktC in Ralstonia eutropha (formerly known as Alcaligenes eutrophus) (Slater et al., J. Bacteriol. 180:1979-1987 (1998); Haywood et al., FEMS Mcrobiology Letters 52:91-96 (1988)). The sequence of the BktB protein is known. The pim operon of Rhodopseudomonas palustris also encodes a beta-ketothiolase, encoded by pimB, predicted to catalyze this transformation in the degradative direction during benzoyl-CoA degradation (Harrison et al., Microbiology 151:727-736 (2005)). A beta-ketothiolase enzyme in S. aciditrophicus was identified by sequence homology to bktB (43% identity, evalue=1e-93).

GenBank Gene name GI# Accession # Organism bktB 11386745 YP_725948 Ralstonia eutropha pimB 39650633 CAE29156 Rhodopseudomonas palustris syn_02642 85860483 YP_462685.1 Syntrophus aciditrophicus

Additional enzymes include beta-ketothiolases that are known to convert two molecules of acetyl-CoA into acetoacetyl-CoA (EC 2.1.3.9). Exemplary acetoacetyl-CoA thiolase enzymes include the gene products of atoB from E. coli (Martin et al., Nat. Biotechnol 21:796-802 (2003)), thlA and thlB from C. acetobutylicum (Hanai et al., Appl Environ Microbiol 73:7814-7818 (2007); Winzer et al., J. Mol. Microbiol Biotechnol 2:531-541(2000)), and ERG10 from S. cerevisiae (Hiser et al., J Biol. Chem. 269:31383-31389(1994)).

GenBank Gene name GI# Accession # Organism atoB 16130161 NP_416728 Escherichia coli thlA 15896127 NP_349476.1 Clostridium acetobutylicum thlB 15004782 NP_149242.1 Clostridium acetobutylicum ERG10 6325229 NP_015297 Saccharomyces cerevisiae

Step C, FIG. 2: 3-Oxoglutaryl-CoA Reductase (Ketone-Reducing)

Exemplary genes and gene products for catalyzing the 3-oxoglutaryl-CoA reductase steps that converte 3-oxoglutaryl-CoA to 3-hydroxyglutaryl-CoA are described above in Example I, step I.

Step D: FIG. 2: 3-Hydroxyglutaryl-CoA Reductase (Aldehyde Forming)

Acyl-CoA dehydrogenases that reduce an acyl-CoA to its corresponding aldehyde include fatty acyl-CoA reductase (EC 1.2.1.42, 1.2.1.50), succinyl-CoA reductase (EC 1.2.1.76), acetyl-CoA reductase, butyryl-CoA reductase and propionyl-CoA reductase (EC 1.2.1.3). Aldehyde forming acyl-CoA reductase enzymes with demonstrated activity on acyl-CoA, 3-hydroxyacyl-CoA and 3-oxoacyl-CoA substrates are known in the literature. Several acyl-CoA reductase enzymes are active on 3-hydroxyacyl-CoA substrates. For example, some butyryl-CoA reductases from Clostridial organisms, are active on 3-hydroxybutyryl-CoA and propionyl-CoA reductase of L. reuteri is active on 3-hydroxypropionyl-CoA. An enzyme for converting 3-oxoacyl-CoA substrates to their corresponding aldehydes is malonyl-CoA reductase. Enzymes in this class can be refined using evolution or enzyme engineering methods known in the art to have activity on enoyl-CoA substrates.

Exemplary fatty acyl-CoA reductases enzymes are encoded by acr1 of Acinetobacter calcoaceticus (Reiser, Journal of Bacteriology 179:2969-2975 (1997)) and Acinetobacter sp. M-1 (Ishige et al., Appl. Environ. Microbiol. 68:1192-1195 (2002)). Two gene products from Mycobacterium tuberculosis accept longer chain fatty acyl-CoA substrates of length C16-C18 (Hanninder Singh, U. Central Fla. (2007)). Yet another fatty acyl-CoA reductase is LuxC of Photobacterium phosphoreum (Lee et al, Biochim Biohys Acta 1388:215-22 (1997)). Enzymes with succinyl-CoA reductase activity are encoded by sucD of Clostridium kluyveri (Sohling, J. Bacteriol. 178:871-880 (1996)) and sucD of P. gingivalis (Takahashi, J. Bacteriol 182:4704-4710 (2000)). Additional succinyl-CoA reductase enzymes participate in the 3-hydroxypropionate/4-hydroxybutyrate cycle of thermophilic archaea including Metallosphaera sedula (Berg et al., Science 318:1782-1786 (2007)) and Thermoproteus neutrophilus (Ramos-Vera et al., J. Bacteriol, 191:4286-4297 (2009)). The M. sedula enzyme, encoded by Msed_0709, is strictly NADPH-dependent and also has malonyl-CoA reductase activity. The T. neutrophilus enzyme is active with both NADPH and NADH. The enzyme acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by bphG, is yet another as it has been demonstrated to oxidize and acylate acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and formaldehyde (Powlowski, J. Bacteriol. 175:377-385 (1993)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxidize the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya, J. Gen. Appl. Microbiol. 18:43-55 (1972); and Koo et al., Biotechnol Lett. 27:505-510 (2005)). Butyraldehyde dehydrogenase catalyzes a similar reaction, conversion of butyryl-CoA to butyraldehyde, in solventogenic organisms such as Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci Biotechnol Biochem., 71:58-68 (2007)). Exemplary propionyl-CoA reductase enzymes include pduP of Salmonella typhimurium LT2 (Leal, Arch. Microbiol. 180:353-361(2003)) and eutE from E. coli (Skraly, WO Patent No. 2004/024876). The propionyl-CoA reductase of Salmonella typhimurium LT2, which naturally converts propionyl-CoA to propionaldehyde, also catalyzes the reduction of 5-hydroxyvaleryl-CoA to 5-hydroxypentanal (WO 2010/068953A2). The propionaldehyde dehydgenase of Lactobacillus reuteri, PduP, has a broad substrate range that includes butyraldehyde, valeraldehyde and 3-hydroxypropionaldehyde (Luo et al, Appl Microbiol Biotech, 89: 697-703 (2011). Additionally, some acyl-ACP reductase enzymes such as the orf1594 gene product of Synechococcus elongatus PCC7942 also exhibit aldehyde-forming acyl-CoA reductase activity (Schirmer et al, Science, 329: 559-62 (2010)).

Protein GenBank ID GI Number Organism acr1 YP_047869.1 50086359 Acinetobacter calcoaceticus acr1 AAC45217 1684886 Acinetobacter baylyi acr1 BAB85476.1 18857901 Acinetobacter sp. Strain M-1 Rv1543 NP_216059.1 15608681 Mycobacterium tuberculosis Rv3391 NP_217908.1 15610527 Mycobacterium tuberculosis LUXC AAT00788.1 46561111 Photobacterium phosphoreum MSED_0709 YP_001190808.1 146303492 Metallosphaera sedula Tneu_0421 ACB39369.1 170934108 Thermoproteus neutrophilus sucD P38947.1 172046062 Clostridium kluyveri sucD NP_904963.1 34540484 Porphyromonas gingivalis bphG BAA03892.1 425213 Pseudomonas sp adhE AAV66076.1 55818563 Leuconostoc mesenteroides bld AAP42563.1 31075383 Clostridium saccharoperbutylacetonicum pduP NP_460996 16765381 Salmonella typhimurium LT2 eutE NP_416950 16130380 Escherichia coli pduP CCC03595.1 337728491 Lactobacillus reuteri

Additionally, some acyl-ACP reductase enzymes such as the orf1594 gene product of Synechococcus elongatus PCC7942 also exhibit aldehyde-forming acyl-CoA reductase activity (Schirmer et al, Science, 329: 559-62 (2010)). The S. elongates PCC7942 acyl-ACP reductase is coexpressed with an aldehyde decarbonylase in an operon that appears to be conserved in a majority of cyanobacterial organisms. This enzyme, expressed in E. coli together with the aldehyde decarbonylase, conferred the ability to produce alkanes. The P. marinus AAR was also cloned into E. coli and, together with a decarbonylase, demonstrated production of alkanes (see, e.g., US Application 2011/0207203).

Gene GenBank ID GI Number Organism orf1594 YP_400611.1 81300403 Synechococcus elongatus PCC7942 PMT9312_0533 YP_397030.1 78778918 Prochlorococcus marinus MIT 9312 syc0051_d YP_170761.1 56750060 Synechococcus elongatus PCC 6301 Ava_2534 YP_323044.1 75908748 Ambaena variabilis ATCC 29413 alr5284 NP_489324.1 17232776 Nostoc sp. PCC 7120 Aazo 3370 YP_003722151.1 298491974 Nostoc azollae Cyan7425_0399 YP_002481152.1 220905841 Cyanothece sp. PCC 7425 N9414_21225 ZP_01628095.1 119508943 Nodularia spumigena CCY9414 L8106 07064 ZP_01619574.1 119485189 Lyngbya sp. PCC 8106

An additional enzyme type that converts an acyl-CoA to its corresponding aldehyde is malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde. Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archaeal bacteria (Berg, Science 318:1782-1786 (2007); and Thauer, Science 318:1732-1733 (2007)). The enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus sp. (Alber et al., J. Bacteriol. 188:8551-8559 (2006); and Hugler, J. Bacteriol. 184:2404-2410 (2002)). The enzyme is encoded by Msed_0709 in Metallosphaera sedula (Alber et al., J. Bacteriol. 188:8551-8559 (2006); and Berg, Science 318:1782-1786 (2007)). A gene encoding a malonyl-CoA reductase from Sulfolobus tokodaii was cloned and heterologously expressed in E. coli (Alber et al., J. Bacteriol 188:8551-8559 (2006). This enzyme has also been shown to catalyze the conversion of methylmalonyl-CoA to its corresponding aldehyde (WO2007141208 (2007)). Although the aldehyde dehydrogenase functionality of these enzymes is similar to the bifunctional dehydrogenase from Chloroflexus aurantiacus, there is little sequence similarity. Both malonyl-CoA reductase enzyme candidates have high sequence similarity to aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the reduction and concurrent dephosphorylation of aspartyl-4-phosphate to aspartate semialdehyde. Additional gene candidates can be found by sequence homology to proteins in other organisms including Sulfolobus solfataricus and Sulfolobus acidocaldarius and have been listed below. Yet another candidate for CoA-acylating aldehyde dehydrogenase is the ald gene from Clostridium beijerinckii (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999). This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes. This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth, Appl. Environ. Microbiol. 65:4973-4980 (1999).

Gene GenBank ID GI Number Organism Msed_0709 YP_001190808.1 146303492 Metallosphaera sedula mcr NP_378167.1 15922498 Sulfolobus tokodaii asd-2 NP_343563.1 15898958 Sulfolobus solfataricus Saci_2370 YP_256941.1 70608071 Sulfolobus acidocaldarius Ald AAT66436 49473535 Clostridium beijerinckii eutE AAA80209 687645 Salmonella typhimurium eutE NP_416950 16130380 Escherichia coli

Step E, FIG. 2: 3-Hydroxy-5-Oxopentanoate Reductase

The reduction of 3-hydroxy 5-oxopentenoate to 3,5-dihydroxypentanoate can be catalyzed by an aldehyde reductase.

Exemplary genes encoding enzymes that catalyze the conversion of an aldehyde to alcohol (e.g., alcohol dehydrogenase or equivalently aldehyde reductase) include alrA encoding a medium-chain alcohol dehydrogenase for C2-C14 (Tani et al., Appl. Environ. Microbiol. 66:5231-5235 (2000)), ADH2 from Saccharomyces cerevisiae (Atsumi et al., Nature 451:86-89 (2008)), yqhD from E. coli which has preference for molecules longer than C(3) (Sulzenbacher et al., J Mol Biol 342:489-502 (2004)), and bdh I and bdh II from C. acetobutylicum which converts butyryaldehyde into butanol (Walter et al., 174:7149-7158 (1992)). The gene product of yqhD catalyzes the reduction of acetaldehyde, malondialdehyde, propionaldehyde, butyraldehyde, and acrolein using NADPH as the cofactor (Perez et al., 283:7346-7353 (2008); Perez et al., J Biol. Chem. 283:7346-7353 (2008)). The adhA gene product from Zymomonas mobilisE has been demonstrated to have activity on a number of aldehydes including formaldehyde, acetaldehyde, propionaldehyde, butyraldehyde, and acrolein (Kinoshita et al., Appl Microbiol Biotechnol 22:249-254 (1985)). Additional aldehyde reductase candidates are encoded by bdh in C. saccharoperbutylacetonicum and Cbei_1722, Cbei_2181 and Cbei_2421 in C. beijerinckii.

Protein GENBANK ID GI NUMBER ORGANISM alrA BAB12273.1 9967138 Acinetobacter sp. stain M-1 ADH2 NP_014032.1 6323961 Saccharomyces cerevisiae yqhD NP_417484.1 16130909 Escherichia coli bdh I NP_349892.1 15896543 Clostridium acetobutylicum bdh II NP_349891.1 15896542 Clostridium acetobutylicum adhA YP_162971.1 56552132 Zymomonas mobilis bdh BAF45463.1 124221917 Clostridium saccharoperbutylacetonicum Cbei_1722 YP_001308850 150016596 Clostridium beijerinckii Cbei_2181 YP_001309304 150017050 Clostridium beijerinckii Cbei 2421 YP_001309535 150017281 Clostridium beijerinckii

Enzymes exhibiting 4-hydroxybutyrate dehydrogenase activity (EC 1.1.1.61) also fall into this category. Such enzymes have been characterized in Ralstonia eutropha (Bravo et al., 49:379-387 (2004)), Clostridium kluyveri (Wolff et al., Protein Expr. Purif 6:206-212 (1995)) and Arabidopsis thaliana (Breitkreuz et al., 278:41552-41556 (2003)). The A. thaliana enzyme was cloned and characterized in yeast (Breitkreuz et al., J Biol. Chem. 278:41552-41556 (2003)). Yet another gene is the alcohol dehydrogenase adhI from Geobacillus thermoglucosidasius (Jeon et al., J Biotechnol 135:27-133_(2008)).

Protein GenBank ID GI number Organism 4hbd YP_726053.1 113867564 Ralstonia eutropha H16 4hbd L21902.1 146348486 Clostridium kluyveri DSM 555 4hbd Q94B07 75249805 Arabidopsis thaliana adhI AAR91477.1 40795502 Geobacillus thermoglucosidasius

Another exemplary enzyme is 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) which catalyzes the reversible oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde. This enzyme participates in valine, leucine and isoleucine degradation and has been identified in bacteria, eukaryotes, and mammals. The enzyme encoded by P84067 from Thermus thermophilus HB8 has been structurally characterized (Lokanath et al., 352:905-17 (2005)). The reversibility of the human 3-hydroxyisobutyrate dehydrogenase was demonstrated using isotopically-labeled substrate (Manning et al., 231:481-4 (1985)). Additional genes encoding this enzyme include 3hidh in Homo sapiens (Hawes et al., 324:218-228 (2000)) and Oryctolagus cuniculus (Hawes et al., Methods Enzymol. 324:218-228 (2000); Chowdhury et al., Biosci. Biotechnol Biochem. 60:2043-2047 (1996)), mmsB in Pseudomonas aeruginosa and Pseudomonas putida, and dhat in Pseudomonas putida (Aberhart et al., J Chem. Soc. [Perkin 1]6:1404-1406 (1979); Chowdhury et al., Biosci. Biotechnol Biochem. 60:2043-2047 (1996); Chowdhury et al., Biosci. Biotechnol Biochem. 67:438-441(2003)). Several 3-hydroxyisobutyrate dehydrogenase enzymes have been characterized in the reductive direction, including mmsB from Pseudomonas aeruginosa (Gokam et al., (2008)) and mmsB from Pseudomonas putida.

Protein GenBank ID GI number Organism P84067 P84067 75345323 Thermus thermophilus 3hidh P31937.2 12643395 Homo sapiens 3hidh P32185.1 416872 Oryctolagus cuniculus mmsB NP_746775.1 26991350 Pseudomonas putida mmsB P28811.1 127211 Pseudomonas aeruginosa dhat Q59477.1 2842618 Pseudomonas putida

3-Hydroxypropionate dehydrogenase, also known as malonate semialdehyde reductase, catalyzes the reversible conversion of malonic semialdehyde to 3-HP. An NADH-dependent 3-hydroxypropionate dehydrogenase is thought to participate in beta-alanine biosynthesis pathways from propionate in bacteria and plants (Rathinasabapathi B., 159:671-674 (2002); Stadtman, J. Am. Chem. Soc. 77:5765-5766 (1955)). An NADPH-dependent malonate semialdehyde reductase catalyzes the reverse reaction in autotrophic CO-fixing bacteria. The enzyme activity has been detected in Metallosphaera sedula. (Alber et al., 188:8551-8559 (2006)). Several 3-hydroxyisobutyrate dehydrogenase enzymes exhibit 3-hydroxypropionate dehydrogenase activity. Three genes exhibiting this activity are mmsB from Pseudomonas aeruginosa PAO1 (Gokam et al., (2008)), mmsB from Pseudomonas putida KT2440 and mmsB from Pseudomonas putida E23 (Chowdhury et al., 60:2043-2047(1996)).

Protein GenBank ID GI number Organism mmsB NP_252259.1 15598765 Pseudomonas putida mmsB NP_746775.1 26991350 Pseudomonas aeruginosa mmsB JC7926 60729613 Pseudomonas putida

Homoserine dehydrogenase (EC 1.1.1.13) catalyzes the NAD(P)H-dependent reduction of aspartate semialdehyde to homoserine. In many organisms, including E. coli, homoserine dehydrogenase is a bifunctional enzyme that also catalyzes the ATP-dependent conversion of aspartate to aspartyl-4-phosphate (Starnes et al., 11:677-687 (1972))1973)). The functional domains are catalytically independent and connected by a linker region (Sibilli et al., 256:10228-10230 (1981)) and both domains are subject to allosteric inhibition by threonine. The homoserine dehydrogenase domain of the E. coli enzyme, encoded by thrA, was separated from the aspartate kinase domain, characterized, and found to exhibit high catalytic activity and reduced inhibition by threonine (James et al., 41:3720-3725 (2002)). This can be applied to other bifunctional threonine kinases including, for example, hom1 of Lactobacillus plantarum (Cahyanto et al., 152:105-112 (2006)) and Arabidopsis thaliana. The monofunctional homoserine dehydrogenases encoded by hom6 in S. cerevisiae (Jacques et al., 1544:28-41(2001)) and hom2 in Lactobacillus plantarum (Cahyanto et al., Microbiology 152:105-112 (2006)) have been functionally expressed and characterized in E. coli.

Protein GenBank ID GI number Organism thrA AAC73113.1 1786183 Escherichia coli K12 akthr2 O81852 75100442 Arabidopsis thaliana hom6 CAA89671 1015880 Saccharomyces cerevisiae hom1 CAD64819 28271914 Lactobacillus plantarum hom2 CAD63186 28270285 Lactobacillus plantarum

Step F, FIG. 2: 3-Hydroxyglutaryl-CoA Reductase (Alcohol Forming)

Bifunctional oxidoreductases convert an acyl-CoA to its corresponding alcohol. Enzymes with this activity are required to convert 3-hydroxygloutaryl-CoA to 3,5-dihydroxypentanoate.

Exemplary bifunctional oxidoreductases that convert an acyl-CoA to alcohol include those that transform substrates such as acetyl-CoA to ethanol (e.g., adE from E. coli (Kessler et al., FEBS. Lett. 281:59-63 (1991))) and butyryl-CoA to butanol (e.g. adhE2 from C. acetobutylicum (Fontaine et al., J. Bacteriol. 184:821-830 (2002))). The C. acetobutylicum enzymes encoded by bdh I and bdh II (Walter, et al., Bacteriol. 174:7149-7158 (1992)), reduce acetyl-CoA and butyryl-CoA to ethanol and butanol, respectively. In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxide the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya et al., J. Gen. Appl. Microbiol. 18:43-55 (1972); Koo et al., Biotechnol Lett, 27:505-510 (2005)). Another exemplary enzyme can convert malonyl-CoA to 3-HP. An NADPH-dependent enzyme with this activity has characterized in Chloroflexus aurantiacus where it participates in the 3-hydroxypropionate cycle (Hugler et al., J. Bacteriol, 184:2404-2410 (2002); Strauss et al., Eur J Biochem, 215:633-643 (1993)). This enzyme, with a mass of 300 kDa, is highly substrate-specific and shows little sequence similarity to other known oxidoreductases (Hugler et al., supra). No enzymes in other organisms have been shown to catalyze this specific reaction; however there is bioinformatic evidence that other organisms may have similar pathways (Klatt et al., Env Microbiol, 9:2067-2078 (2007)). Enzyme candidates in other organisms including Roseiflexus castenholzii, Ethrobacter sp. NAP1 and marine gamma proteobacterium HTCC28 can be inferred by sequence similarity.

Protein GenBank ID GI Number Organism adhE NP_415757.1 16129202 Escherichia coli adhE2 AAK09379.1 12958626 Clostridium acetobutylicum bdh I NP_349892.1 15896543 Clostridium acetobutylicum bdh II NP_349891.1 15896542 Clostridium acetobutylicum adhE AAV66076.1 55818563 Leuconostoc mesenteroides mcr AAS20429.1 42561982 Chloroflexus aurantiacus Rcas_2929 YP_001433009.1 156742880 Roseiflexus castenholzii NAP1 02720 ZP_01039179.1 85708113 Erythrobacter sp. NAP1 MGP2080 00535 ZP_01626393.1 119504313 marine gamma proteobacterium HTCC2080

Longer chain acyl-CoA molecules can be reduced to their corresponding alcohols by enzymes such as the jojoba (Simmondsia chinensis) FAR which encodes an alcohol-forming fatty acyl-CoA reductase. Its overexpression in E. coli resulted in FAR activity and the accumulation of fatty alcohol (Metz et al., Plant Physiol, 122:635-644 (2000)). Bifunctional prokaryotic FAR enzymes are found in Marinobacter aquaeolei VT8 (Hofvander et al, FEBS Lett 3538-43 (2011)), Marinobacter algicola and Oceanobacter strain RED65 (US Pat Appl 20110000125).

Protein GenBank ID GI Number Organism FAR AAD38039.1 5020215 Simmondsia chinensis FAR YP_959486.1 120555135 Marinobacter aquaeolei

Another candidate for catalyzing these steps is 3-hydroxy-3-methylglutaryl-CoA reductase (or HMG-CoA reductase). This enzyme naturally reduces the CoA group in 3-hydroxy-3-methylglutaryl-CoA to an alcohol forming mevalonate. The hmgA gene of Sulfolobus solfataricus, encoding 3-hydroxy-3-methylglutaryl-CoA reductase, has been cloned, sequenced, and expressed in E. coli (Bochar et al., J Bacteriol. 179:3632-3638 (1997)). S. cerevisiae also has two HMG-CoA reductases in it (Basson et al., Proc. Natl. Acad. Sci. USA 83:5563-5567 (1986)). The gene has also been isolated from Arabidopsis thaliana and has been shown to complement the HMG-COA reductase activity in S. cerevisiae (Learned et al., Proc. Natl. Acad Sci. USA 86:2779-2783 (1989)).

Protein GenBank ID GI Number Organism HMG1 CAA86503.1 587536 Saccharomyces cerevisiae HMG2 NP_013555 6323483 Saccharomyces cerevisiae HMG1 CAA70691.1 1694976 Arabidopsis thaliana hmgA AAC45370.1 2130564 Sulfolobus solfataricus

4-Hydroxybutyryl-CoA reductase (alcohol forming) enzymes are bifunctional oxidoreductases that convert an 4-hydroxybutyryl-CoA to 1,4-butanediol. Enzymes with this activity include adhE from E. coli, adhE2 from C. acetobutylicum (Fontaine et al., J. Bacteriol. 184:821-830 (2002)) and the C. acetobutylicum enzymes encoded by bdhI and bdh II (Walter, et al., J. Bacteriol. 174:7149-7158 (1992)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxide the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya et al., J. Gen. Appl. Microbiol. 18:43-55 (1972); Koo et al., Biotechnol Lett, 27:505-510 (2005)).

Protein GenBank ID GI Number Organism adhE NP_415757.1 16129202 Escherichia coli adhE2 AAK09379.1 12958626 Clostridium acetobutylicum bdh I NP_349892.1 15896543 Clostridium acetobutylicum bdh II NP_349891.1 15896542 Clostridium acetobutylicum adhE AAV66076.1 55818563 Leuconostoc mesenteroides adhE NP_781989.1 28211045 Clostridium tetani adhE NP_563447.1 18311513 Clostridium perfringens adhE YP_001089483.1 126700586 Clostridium difficile

Steps J, M, FIG. 2: 3,5-Dihydroxypentanoate Ligase, 5-Hydroxypent-2-Enoate Ligase

Exemplary genes and gene products for catalyzing the CoA ligase steps that convert 3,5-dihydroxypentanoate to 3,5-dihdyroxypentannoyl-CoA and 5-hydroxypent-2-enoyl-CoA are described above in Example I, step G and step J.

Steps K, N, and Q: FIG. 2: 3,5-Dihydroxypentanoate:Acetyl-CoA CoA Transferase, 5-Hydroxypent-2-Enoate:Acetyl-CoA CoA Transferase, 2,4-Pentadienoyl-CoA:Acetyl-CoA CoA Transferase

Exemplary genes and gene products for catalyzing the CoA transferase steps that convert the substrates and products of Steps K, 1N, and Q in FIG. 2 are described above in Example I, Steps H, K and N.

Step P, FIG. 2: 2,4-Pentadienoyl-CoA CoA Hydrolase

Exemplary genes and gene products for catalyzing the CoA hydrolase steps that convert 2,4-pentadienoyl-CoA into 2,4-pentadienoate are described above in Example I, step M.

Step I, FIG. 2: 24-Pentadienoate Decarboxylase

Exemplary genes and gene products for catalyzing the decarboxylase steps that convert penta-2,4-dienoate to butadiene are described above in Example I, step F.

Step L, FIG. 2: 3,5-Dihydroxypentanoyl-CoA Dehydratase

Exemplary genes and gene products for catalyzing the dehydratase steps that convert 3,5-dihydroxypentanoyl-CoA into 5-hydroxyoent-2-enoyl-CoA belong to the category of 3-hydroxyacyl-CoA dehydratases, which are described in Example I, step L.

Step O, FIG. 2: 5-Hydroxypent-2-Enoyl-CoA Hydrolase

Acyl CoA dehydratases can catalyze the dehydration of 5-hydroxypent-2-enoyl-CoA into 2,4-pentadienoyl-CoA. Specifically, an enzyme that can catalzye this transformation has been described in Buckel, Appl Microbiol Biotechnol. 2001 October; 57(3):263-7. 5-hydroxyvaleryl-CoA dehydrogenase/dehydratase has been described from Clostridium viride, previously called Clostridium aminovalericum. This enzyme can first oxidize 5-hydroxyvaleryl-CoA to 5-hydroxypentenoyl-CoA. This is subsequently dehydrated to form 2,4-pentadienoyl-CoA. The crystal structure of the dehydratase has been solved to 2.2 A⁰ resolution. Eikmanns et al., Proteins. 1994 July; 19(3):269-71, Eikmanns and Buckel, Eur J Biochem, 1991 May 8; 197(3):661-8.

Other gene candidates in the enzyme class 4.2.1 can catalyze this transformation. Several candidates are listed in Example I, step L.

Steps G and H, FIG. 2: 3,5-Dihydroxypentanoate Dehydratase and 5-Hydroxypent-2-Enoate Dehydratase

Exemplary dehydratase that can catalyze dehydration of 3,5-dihydroxypentanoate to 5-hydroxy pent-2-enoate and of 5-hydroxy pent-2-enoate to pent-2,4-dienoate are described in Example I, step E.

Step S, FIG. 2: 3-Hydroxy-5-Oxopentanoate Synthase

The reduction of 3-hydroxyglutarylphosphate to 3-hydroxy-5-oxopentanoate can be catalyzed by an oxidoreductase or phosphate reductase in the EC class 1.2.1. Exemplary phosphonate reductase enzymes include glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12), aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) acetylglutaylphosphate reductase (EC 1.2.1.38) and glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.-). Aspartate semialdehyde dehydrogenase (ASD, EC 1.2.1.11) catalyzes the NADPH-dependent reduction of 4-aspartyl phosphate to aspartate-4-semialdehyde. ASD participates in amino acid biosynthesis and recently has been studied as an antimicrobial target (Hadfield et al., Biochemistry 40:14475-14483 (2001)). The E. coli ASD structure has been solved (Hadfield et al., J Mol. Biol. 289:991-1002 (1999)) and the enzyme has been shown to accept the alternate substrate beta-3-methylaspartyl phosphate (Shames et al., J Biol. Chem. 259:15331-15339 (1984)). The Haemophilus influenzae enzyme has been the subject of enzyme engineering studies to alter substrate binding affinities at the active site (Blanco et al., Acta Crystallogr. D. Biol. Crystallogr. 60:1388-1395 (2004); Blanco et al., Acta Crystallogr. D. Biol. Crystallogr. 60:1808-1815 (2004)). Other ASD candidates are found in Mycobacterium tuberculosis (Shafiani et al., J Appl Microbiol 98:832-838 (2005)), Methanococcus jannaschii (Faehnle et al., J Mol. Biol. 353:1055-1068 (2005)), and the infectious microorganisms Vibrio cholera and Heliobacter pylori (Moore et al., Protein Expr. Purif 25:189-194 (2002)). A related enzyme candidate is acetylglutamylphosphate reductase (EC 1.2.1.38), an enzyme that naturally reduces acetylglutamylphosphate to acetylglutamate-5-semialdehyde, found in S. cerevisiae (Pauwels et al., Eur. J Biochem. 270:1014-1024 (2003)), B. subtilis (O'Reilly et al., Microbiology 140 (Pt 5):1023-1025 (1994)), E. coli (Parsot et al., Gene. 68:275-283 (1988)), and other organisms. Additional phosphate reductase enzymes of E. coli include glyceraldehyde 3-phosphate dehydrogenase (gapA (Branlant et al., Eur. J Biochem. 150:61-66 (1985))) and glutamate-5-semialdehyde dehydrogenase (proA (Smith et al., J. Bacteriol. 157:545-551(1984))). Genes encoding glutamate-5-semialdehyde dehydrogenase enzymes from Salmonella typhimurium (Mahan et al., J. Bacteriol. 156:1249-1262 (1983)) and Campylobacter jejuni (Louie et al., Mol. Gen. Genet. 240:29-35 (1993)) were cloned and expressed in E. coli.

Protein GenBank ID GI Number Organism asd NP_417891.1 16131307 Escherichia coli asd YP_248335.1 68249223 Haemophilus influenzae asd AAB49996 1899206 Mycobacterium tuberculosis VC2036 NP_231670 15642038 Vibrio cholera asd YP_002301787.1 210135348 Heliobacter pylori ARG5,6 NP_010992.1 6320913 Saccharomyces cerevisiae argC NP_389001.1 16078184 Bacillus subtilis argC NP_418393.1 16131796 Escherichia coli gapA P0A9B2.2 71159358 Escherichia coli proA NP_414778.1 16128229 Escherichia coli proA NP_459319.1 16763704 Salmonella typhimurium proA P53000.2 9087222 Campylobacter jejuni

Step R, FIG. 2: Phosphate-3-Hydroxyglutaryl Transferase

Exemplary phosphate-transferring acyltransferases that can convert 3-hydroxyglutaryl-CoA into 3-hydroxyglutaryl phosphate include phosphotransacetylase (EC 2.3.1.8) and phosphotransbutyrylase (EC 2.3.1.19). The pta gene from E. coli encodes a phosphotransacetylase that reversibly converts acetyl-CoA into acetyl-phosphate (Suzuki, Biochim. Biophys. Acta 191:559-569 (1969)). This enzyme can also utilize propionyl-CoA as a substrate, forming propionate in the process (Hesslinger et al., Mol. Microbiol 27:477-492 (1998)). Other phosphate acetyltransferases that exhibit activity on propionyl-CoA are found in Bacillus subtilis (Rado et al., Biochim. Biophys. Acta 321:114-125 (1973)), Clostridium kluyveri (Stadtman, Methods Enzymol 1:596-599 (1955)), and Thermotoga maritima (Bock et al., J. Bacteriol. 181:1861-1867 (1999)). Similarly, the ptb gene from C. acetobutylicum encodes phosphotransbutyrylase, an enzyme that reversibly converts butyryl-CoA into butyryl-phosphate (Wiesenbom et al., Appl Environ. Microbiol 55:317-322 (1989); Walter et al., Gene 134:107-111(1993)). Additional ptb genes are found in butyrate-producing bacterium L2-50 (Louis et al., J. Bacteriol. 186:2099-2106 (2004)) and Bacillus megaterium (Vazquez et al., Curr. Microbiol 42:345-349 (2001)).

Protein GenBank ID GI Number Organism pta NP_416800.1 71152910 Escherichia coli pta P39646 730415 Bacillus subtilis pta A5N801 146346896 Clostridium kluyveri pta Q9X0L4 6685776 Thermotoga maritima ptb NP_349676 34540484 Clostridium acetobutylicum ptb AAR19757.1 38425288 butyrate-producing bacterium L2-50 ptb CAC07932.1 10046659 Bacillus megaterium

Example III Formate Assimilation Pathways

This example describes enzymatic pathways for converting pyruvate to formaldehyde, and optionally in combination with producing acetyl-CoA and/or reproducing pyruvate.

Step E, FIG. 3: Formate Reductase

The conversion of formate to formaldehyde can be carried out by a formate reductase (step E, FIG. 3). A suitable enzyme for these transformations is the aryl-aldehyde dehydrogenase, or equivalently a carboxylic acid reductase, from Nocardia iowensis. Carboxylic acid reductase catalyzes the magnesium, ATP and NADPH-dependent reduction of carboxylic acids to their corresponding aldehydes (Venkitasubramanian et al., J Biol. Chem. 282:478-485 (2007)). This enzyme, encoded by car, was cloned and functionally expressed in E. coli (Venkitasubramanian et al., J. Biol. Chem. 282:478-485 (2007)). Expression of the npt gene product improved activity of the enzyme via post-transcriptional modification. The npt gene encodes a specific phosphopantetheine transferase (PPTase) that converts the inactive apo-enzyme to the active holo-enzyme. The natural substrate of this enzyme is vanillic acid, and the enzyme exhibits broad acceptance of aromatic and aliphatic substrates (Venkitasubramanian et al., in Biocatalysis in the Pharmaceutical and Biotechnology Industries, ed. R. N. Patel, Chapter 15, pp. 425-440, CRC Press LLC, Boca Raton, Fla. (2006)). Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism Car AAR91681.1 40796035 Nocardia iowensis (sp. NRRL 5646) Npt ABI83656.1 114848891 Nocardia iowensis (sp. NRRL 5646)

Additional car and npt genes can be identified based on sequence homology.

Protein GenBank ID GI number Organism fadD9 YP_978699.1 121638475 Mycobacterium bovis BCG BCG_2812c YP_978898.1 121638674 Mycobacterium bovis BCG nfa20150 YP_118225.1 54023983 Nocardia farcinica IFM 10152 nfa40540 YP_120266.1 54026024 Nocardia farcinica IFM 10152 SGR 6790 YP_001828302.1 182440583 Streptomyces griseus subsp. griseus NBRC 13350 SGR_665 YP_001822177.1 182434458 Streptomyces griseus subsp. griseus NBRC 13350 MSMEG_2956 YP_887275.1 118473501 Mycobacterium smegmatis MC2 155 MSMEG 5739 YP_889972.1 118469671 Mycobacterium smegmatis MC2 155 MSMEG 2648 YP_886985.1 118471293 Mycobacterium smegmatis MC2 155 MAP1040c NP_959974.1 41407138 Mycobacterium avium subsp. paratuberculosis K-10 MAP2899c NP_961833.1 41408997 Mycobacterium avium subsp. paratuberculosis K-10 MMAR_2117 YP_001850422.1 183982131 Mycobacterium marinum M MMAR 2936 YP_001851230.1 183982939 Mycobacterium marinum M MMAR 1916 YP_001850220.1 183981929 Mycobacterium marinum M TpauDRAFT_33060 ZP_04027864.1 227980601 Tsukamurella paurometabola DSM 20162 TpauDRAFT_20920 ZP_04026660.1 227979396 Tsukamurella paurometabola DSM 20162 CPCC7001_1320 ZP_05045132.1 254431429 Cyanobium PCC7001 DDBDRAFT_0187729 XP_636931.1 66806417 Dictyostelium discoideum AX4

An additional enzyme candidate found in Streptomyces griseus is encoded by griC and griD genes. This enzyme is believed to convert 3-amino-4-hydroxybenzoic acid to 3-amino-4-hydroxybenzaldehyde as deletion of either griC or griD led to accumulation of extracellular 3-acetylamino-4-hydroxybenzoic acid, a shunt product of 3-amino-4-hydroxybenzoic acid metabolism (Suzuki, et al., J. Antibiot. 60(6):380-387 (2007)). Co-expression of griC and griD with SGR_665, an enzyme similar in sequence to the Nocardia iowensis npt, can be beneficial. Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism griC YP_001825755.1 182438036 Streptomyces griseus subsp. griseus NBRC 13350 griD YP_001825756.1 182438037 Streptomyces griseus subsp. griseus NBRC 13350

An enzyme with similar characteristics, alpha-aminoadipate reductase (AAR, EC 1.2.1.31), participates in lysine biosynthesis pathways in some fungal species. This enzyme naturally reduces alpha-aminoadipate to alpha-aminoadipate semialdehyde. The carboxyl group is first activated through the ATP-dependent formation of an adenylate that is then reduced by NAD(P)H to yield the aldehyde and AMP. Like CAR, this enzyme utilizes magnesium and requires activation by PPTase. Enzyme candidates for AAR and its corresponding PPTase are found in Saccharomyces cerevisiae (Morris et al., Gene 98:141-145 (1991)), Candida albicans(Guo et al, Mol. Genet. Genomics 269:271-279(2003)), and Schizosaccharomyces pombe (Ford et al., Curr. Genet. 28:131-137(1995)). The AAR from S. pombe exhibited significant activity when expressed in E. coli (Guo et al., Yeast 21:1279-1288 (2004)). The AAR from Penicillium chrysogenum accepts S-carboxymethyl-L-cysteine as an alternate substrate, but did not react with adipate, L-glutamate or diaminopimelate (Hijaubia et al., J. Biol. Chem. 2788250-8256 (2003)). Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism LYS2 AAA34747.1 171867 Saccharomyces cerevisiae LYS5 P50113.1 1708896 Saccharomyces cerevisiae LYS2 AAC02241.1 2853226 Candida albicans LYS5 AAO26020.1 28136195 Candida albicans Lys1p P40976.3 13124791 Schizosaccharomyces pombe Lys7p Q10474.1 1723561 Schizosaccharomyces pombe Lys2 CAA74300.1 3282044 Penicillium chrysogenum

Tani et al (Agric Biol Chem, 1978, 42:63-68; Agric Biol Chem, 1974, 38:2057-2058) showed that purified enzymes from Escherichia coli strain B could reduce the sodium salts of different organic acids (e.g. formate, glycolate, acetate, etc.) to their respective aldehydes (e.g. formaldehyde, glycoaldehyde, acetaldehyde, etc.). Of three purified enzymes examined by Tani et al (1978), only the “A” isozyme was shown to reduce formate to formaldehyde. Collectively, this group of enzymes was originally termed glycoaldehyde dehydrogenase; however, their novel reductase activity led the authors to propose the name glycolate reductase as being more appropriate (Morita et al, Agric Biol Chem, 1979, 43: 185-186). Morita et al (Agric Biol Chem, 1979, 43: 185-186) subsequently showed that glycolate reductase activity is relatively widespread among microorganisms, being found for example in: Pseudomonas, Agrobacterium, Escherichia, Flavobacterium, Micrococcus, Staphylococcus, Bacillus, and others. Without wishing to be bound by any particular theory, it is believed that some of these glycolate reductase enzymes are able to reduce formate to formaldehyde.

Any of these CAR or CAR-like enzymes can exhibit formate reductase activity or can be engineered to do so.

Step F, FIG. 3: Formate Ligase, Formate Transferase, Formate Synthetase

The acylation of formate to formyl-CoA is catalyzed by enzymes with formate transferase, synthetase, or ligase activity (Step F, FIG. 3). Formate transferase enzymes have been identified in several organisms including Escherichia coli (Toyota, et al., J. Bacteriol. 2008 April; 190(7):2556-64), Oxalobacter formigenes (Toyota, et al., J Bacteriol. 2008 April; 190(7):2556-64; Baetz et al., J. Bacteriol. 1990 July; 172(7):3537-40; Ricagno, et al., EMBO J. 2003 Jul. 1; 22(13):3210-9)), and Lactobacillus acidophilus (Azcarate-Peril, et al., Appl. Environ. Microbiol. 2006 72(3)1891-1899). Homologs exist in several other organisms. Enzymes acting on the CoA-donor for formate transferase may also be expressed to ensure efficient regeneration of the CoA-donor. For example, if oxalyl-CoA is the CoA donor substrate for formate transferase, an additional transferase, synthetase, or ligase may be required to enable efficient regeneration of oxalyl-CoA from oxalate. Similarly, if succinyl-CoA or acetyl-CoA is the CoA donor substrate for formate transferase, an additional transferase, synthetase, or ligase may be required to enable efficient regeneration of succinyl-CoA from succinate or acetyl-CoA from acetate, respectively.

Protein GenBank ID GI number Organism YfdW NP_416875.1 16130306 Escherichia coli frc O06644.3 21542067 Oxalobacter formigenes frc ZP_04021099.1 227903294 Lactobacillus acidophilus

Suitable CoA-donor regeneration or formate transferase enzymes are encoded by the gene products of cat1, cat2, and cat3 of Clostridium kluyveri. These enzymes have been shown to exhibit succinyl-CoA, 4-hydroxybutyryl-CoA, and butyryl-CoA acetyltransferase activity, respectively (Seedorf et al., Proc. Nat. Acad Sci. USA 105:2128-2133 (2008); Sohling and Gottschalk, J. Bacteriol 178:871-880 (1996)). Similar CoA transferase activities are also present in Trichomonas vaginalis (van Grinsven et al., J Biol. Chem. 283:1411-1418 (2008)) and Trypanosoma brucei (Riviere et al., J Biol. Chem. 279:45337-45346 (2004)). Yet another transferase capable of the desired conversions is butyryl-CoA:acetoacetate CoA-transferase. Exemplary enzymes can be found in Fusobacterium nucleatum (Barker et al., J. Bacteriol. 152(1):201-7 (1982)), Clostridium SB4 (Barker et al., J Biol. Chem. 253(4):1219-25 (1978)), and Clostridium acetobutylicum (Wiesenbom et al., Appl. Environ. Microbiol. 55(2):323-9 (1989)). Although specific gene sequences were not provided for butyryl-CoA:acetoacetate CoA-transferase in these references, the genes FN0272 and FN0273 have been annotated as a butyrate-acetoacetate CoA-transferase (Kapatral et al., J. Bact. 184(7) 2005-2018 (2002)). Homologs in Fusobacterium nucleatum such as FN1857 and FN1856 also likely have the desired acetoacetyl-CoA transferase activity. FN1857 and FN1856 are located adjacent to many other genes involved in lysine fermentation and are thus very likely to encode an acetoacetate:butyrate CoA transferase (Kreimeyer, et al., J Biol. Chem. 282 (10) 7191-7197 (2007)). Additional candidates from Porphyrmonas gingivalis and Thermoanaerobacter tengcongensis can be identified in a similar fashion (Kreimeyer, et al., J Biol. Chem. 282 (10) 7191-7197 (2007)). Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism Cat1 P38946.1 729048 Clostridium kluyveri Cat2 P38942.2 1705614 Clostridium kluyveri Cat3 EDK35586.1 146349050 Clostridium kluyveri TVAG 395550 XP_001330176 123975034 Trichomonas vaginalis G3 Tb11.02.0290 XP_828352 71754875 Trypanosoma brucei FN0272 NP_603179.1 19703617 Fusobacterium nucleatum FN0273 NP_603180.1 19703618 Fusobacterium nucleatum FN1857 NP_602657.1 19705162 Fusobacterium nucleatum FN1856 NP_602656.1 19705161 Fusobacterium nucleatum PG1066 NP_905281.1 34540802 Porphyromonas gingivalis W83 PG1075 NP_905290.1 34540811 Porphyromonas gingivalis W83 IIE0720 NP_622378.1 20807207 Thermoanaerobacter tengcongensis MB4 IIE0721 NP_622379.1 20807208 Thermoanaerobacter tengcongensis MB4

Additional transferase enzymes of interest include the gene products of atoAD from E. coli (Hanai et al., Appl Environ Microbiol 73:7814-7818 (2007)), ctfAB from C. acetobutylicum (Jojima et al., Appl Microbiol Biotechnol 77:1219-1224 (2008)), and ctfAB from Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci. Bioechnol Biochem. 71:58-68 (2007)). Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism AtoA P76459.1 2492994 Escherichia coli AtoD P76458.1 2492990 Escherichia coli CtfA NP_149326.1 15004866 Clostridium acetobutylicum CtfB NP_149327.1 15004867 Clostridium acetobutylicum CtfA AAP42564.1 31075384 Clostridium saccharoperbutylacetonicum CtfB AAP42565.1 31075385 Clostridium saccharoperbutylacetonicum

Succinyl-CoA:3-ketoacid-CoA transferase naturally converts succinate to succinyl-CoA while converting a 3-ketoacyl-CoA to a 3-ketoacid. Exemplary succinyl-CoA:3:ketoacid-CoA transferases are present in Helicobacter pylori (Corthesy-Theulaz et al., J Biol. Chem. 272:25659-25667 (1997)), Bacillus subtilis (Stols et al., Protein. Expr. Purif. 53:396-403 (2007)), and Homo sapiens (Fukao et al., Genomics 68:144-151(2000); Tanaka et al., Mol. Hum. Reprod. 8:16-23 (2002)). Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism HPAG1_0676 YP_627417 108563101 Helicobacter pylori HPAG1_0677 YP_627418 108563102 Helicobacter pylori ScoA NP_391778 16080950 Bacillus subtilis ScoB NP_391777 16080949 Bacillus subtilis OXCT1 NP_000427 4557817 Homo sapiens OXCT2 NP_071403 11545841 Homo sapiens

Two additional enzymes that catalyze the activation of formate to formyl-CoA reaction are AMP-forming formyl-CoA synthetase and ADP-forming formyl-CoA synthetase. Exemplary enzymes, known to function on acetate, are found in E. coli (Brown et al., J. Gen. Microbiol. 102:327-336 (1977)), Ralstonia eutropha (Priefert and Steinbuchel, J. Bacteriol. 174:6590-6599 (1992)), Methanothermobacter thermautotrophicus (Ingram-Smith and Smith, Archaea 2:95-107 (2007)), Salmonella enterica (Gulick et al., Biochemistry 42:2866-2873 (2003)) and Saccharomyces cerevisiae (Jogl and Tong, Biochemistry 43:1425-1431(2004)). Such enzymes may also acylate formate naturally or can be engineered to do so.

Protein GenBank ID GI Number Organism acs AAC77039.1 1790505 Escherichia coli acoE AAA21945.1 141890 Ralstonia eutropha acs1 ABC87079.1 86169671 Methanothermobacter thermautotrophicus acs1 AAL23099.1 16422835 Salmonella enterica ACS1 Q01574.2 257050994 Saccharomyces cerevisiae

ADP-forming acetyl-CoA synthetase (ACD, EC 6.2.1.13) is another candidate enzyme that couples the conversion of acyl-CoA esters to their corresponding acids with the concurrent synthesis of ATP. Several enzymes with broad substrate specificities have been described in the literature. ACD I from Archaeoglobus fulgidus, encoded by AF1211, was shown to operate on a variety of linear and branched-chain substrates including acetyl-CoA, propionyl-CoA, butyryl-CoA, acetate, propionate, butyrate, isobutyryate, isovalerate, succinate, fumarate, phenylacetate, indoleacetate (Musfeldt et al., J. Bacteriol. 184:636-644 (2002)). The enzyme from Haloarcula marismortui (annotated as a succinyl-CoA synthetase) accepts propionate, butyrate, and branched-chain acids (isovalerate and isobutyrate) as substrates, and was shown to operate in the forward and reverse directions (Brasen et al., Arch. Microbiol. 182:277-287 (2004)). The ACD encoded by PAE3250 from hyperthermophilic crenarchaeon Pyrobaculum aerophilum showed the broadest substrate range of all characterized ACDs, reacting with acetyl-CoA, isobutyryl-CoA (preferred substrate) and phenylacetyl-CoA (Brasen et al, supra (2004)). The enzymes from A. fulgidus, H. marismortui and P. aerophilum have all been cloned, functionally expressed, and characterized in E. coli (Musfeldt et al., supra; Brasen et al., supra (2004)). Additional candidates include the succinyl-CoA synthetase encoded by sucCD in E. coli (Buck et al., Biochemistry 24:6245-6252 (1985)) and the acyl-CoA ligase from Pseudomonas putida (Femandez-Valverde et al., Appl. Environ. Microbiol. 59:1149-1154 (1993)). Such enzymes may also acylate formate naturally or can be engineered to do so. Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism AF1211 NP_070039.1 11498810 Archaeoglobus fulgidus DSM 4304 AF1983 NP_070807.1 11499565 Archaeoglobus fulgidus DSM 4304 scs YP_135572.1 55377722 Haloarcula marismortui ATCC 43049 PAE3250 NP_560604.1 18313937 Pyrobaculum aerophilum str. IM2 sucC NP_415256.1 16128703 Escherichia coli sucD AAC73823.1 1786949 Escherichia coli paaF AAC24333.2 22711873 Pseudomonas putida

An alternative method for adding the CoA moiety to formate is to apply a pair of enzymes such as a phosphate-transferring acyltransferase and a kinase. These activities enable the net formation of formyl-CoA with the simultaneous consumption of ATP. An exemplary phosphate-transferring acyltransferase is phosphotransacetylase, encoded by pta. The pta gene from E. coli encodes an enzyme that can convert acetyl-CoA into acetyl-phosphate, and vice versa (Suzuki, T. Biochim. Biophys. Acta 191:559-569 (1969)). This enzyme can also utilize propionyl-CoA instead of acetyl-CoA forming propionate in the process (Hesslinger et al. Mol. Microbiol 27:477-492 (1998)). Homologs exist in several other organisms including Salmonella enterica and Chlamydomonas reinhardtii. Such enzymes may also phosphorylate formate naturally or can be engineered to do so.

Protein GenBank ID GI number Organism Pta NP_416800.1 16130232 Escherichia coli Pta NP_461280.1 16765665 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 PAT2 XP_001694504.1 159472743 Chlamydomonas reinhardtii PAT1 XP_001691787.1 159467202 Chlamydomonas reinhardtii

An exemplary acetate kinase is the E. coli acetate kinase, encoded by ackA (Skarstedt and Silverstein J Biol. Chem. 251:6775-6783 (1976)). Homologs exist in several other organisms including Salmonella enterica and Chlamydomonas reinhardtii. It is likely that such enzymes naturally possess formate kinase activity or can be engineered to have this activity. Information related to these proteins and genes is shown below:

Protein GenBank ID GI number Organism AckA NP_416799.1 16130231 Escherichia coli AckA NP_461279.1 16765664 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ACK1 XP_001694505.1 159472745 Chlamydomonas reinhardtii ACK2 XP_001691682.1 159466992 Chlamydomonas reinhardtii

The acylation of formate to formyl-CoA can also be carried out by a formate ligase. For example, the product of the LSC1 and LSC2 genes of S. cerevisiae and the sucC and sucD genes of E. coli naturally form a succinyl-CoA ligase complex that catalyzes the formation of succinyl-CoA from succinate with the concomitant consumption of one ATP, a reaction which is reversible in vivo (Gruys et al., U.S. Pat. No. 5,958,745, filed Sep. 28, 1999). Such enzymes may also acylate formate naturally or can be engineered to do so. Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism SucC NP_415256.1 16128703 Escherichia coli SucD AAC73823.1 1786949 Escherichia coli LSC1 NP_014785 6324716 Saccharomyces cerevisiae LSC2 NP_011760 6321683 Saccharomyces cerevisiae

Additional exemplary CoA-ligases include the rat dicarboxylate-CoA ligase for which the sequence is yet uncharacterized (Vamecq et al., Biochemical J. 230:683-693 (1985)), either of the two characterized phenylacetate-CoA ligases from P. chrysogenum (Lamas-Maceiras et al., Biochem. J. 395:147-155 (2005); Wang et al., Biochem Biophy Res Commun 360(2):453-458 (2007)), the phenylacetate-CoA ligase from Pseudomonas putida (Martinez-Blanco et al., J Biol. Chem. 265:7084-7090 (1990)), and the 6-carboxyhexanoate-CoA ligase from Bacillus subtilis (Bower et al., J. Bacteriol. 178(14):4122-4130 (1996)). Additional candidate enzymes are acetoacetyl-CoA synthetases from Mus musculus (Hasegawa et al., Biochim. Biophys. Acta 1779:414-419 (2008)) and Homo sapiens (Ohgami et al., Biochem. Pharmacol. 65:989-994 (2003)), which naturally catalyze the ATP-dependent conversion of acetoacetate into acetoacetyl-CoA. 4-Hydroxybutyryl-CoA synthetase activity has been demonstrated in Metallosphaera sedula (Berg et al., Science 318:1782-1786 (2007)). This function has been tentatively assigned to the Msed_1422 gene. Such enzymes may also acylate formate naturally or can be engineered to do so. Information related to these proteins and genes is shown below.

Protein GenBank ID GI number Organism Phl CAJ15517.1 77019264 Penicillium chrysogenum PhlB ABS19624.1 152002983 Penicillium chrysogenum PaaF AAC24333.2 22711873 Pseudomonas putida BioW NP_390902.2 50812281 Bacillus subtilis AACS NP_084486.1 21313520 Mus musculus AACS NP_076417.2 31982927 Homo sapiens Msed 1422 YP_001191504 146304188 Metallosphaera sedula

Step G, FIG. 3: Formyl-CoA Reductase

Several acyl-CoA dehydrogenases are capable of reducing an acyl-CoA (e.g., formyl-CoA) to its corresponding aldehyde (e.g., formaldehyde)(Steps F, FIG. 3). Exemplary genes that encode such enzymes include the Acinetobacter calcoaceticus acr1 encoding a fatty acyl-CoA reductase (Reiser and Somerville, J. Bacteriol. 179:2969-2975 (1997), the Acinetobacter sp. M-1 fatty acyl-CoA reductase (Ishige et al., Appl. Environ. Microbiol. 68:1192-1195 (2002), and a CoA- and NADP-dependent succinate semialdehyde dehydrogenase encoded by the sucD gene in Clostridium kluyveri (Sohling and Gottschalk, J. Bacteriol. 178:871-880 (1996); Sohling and Gottschalk, J Bacteriol. 1778:871-880 (1996)). SucD of P. gingivalis is another succinate semialdehyde dehydrogenase (Takahashi et al., J. Bacteriol. 182:4704-4710 (2000). The enzyme acylating acetaldehyde dehydrogenase in Pseudomonas sp, encoded by bphG, is yet another candidate as it has been demonstrated to oxidize and acylate acetaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde and formaldehyde (Powlowski et al., J. Bacteriol. 175:377-385 (1993)). In addition to reducing acetyl-CoA to ethanol, the enzyme encoded by adhE in Leuconostoc mesenteroides has been shown to oxidize the branched chain compound isobutyraldehyde to isobutyryl-CoA (Kazahaya et al., J. Gen. Appl. Microbiol. 18:45-55 (1972); Koo et al., Biotechnol. Lett. 27:505-510 (2005)). Butyraldehyde dehydrogenase catalyzes a similar reaction, conversion of butyryl-CoA to butyraldehyde, in solventogenic organisms such as Clostridium saccharoperbutylacetonicum(Kosaka et. al., Biosci. Biotechnol. Biochem. 71:58-68 (2007)). Additional aldehyde dehydrogenase enzyme candidates are found in Desulfatibacillum alkenivorans, Citrobacter koseri, Salmonella enterica, Lactobacillus brevis and Bacillus selenitireducens. Such enzymes may be capable of naturally converting formyl-CoA to formaldehyde or can be engineered to do so.

Protein GenBank ID GI number Organism acr1 YP_047869.1 50086355 Acinetobacter calcoaceticus acr1 AAC45217 1684886 Acinetobacter baylyi acr1 BAB85476.1 18857901 Acinetobacter sp. Strain M-1 sucD P38947.1 172046062 Clostridium kluyveri sucD NP_904963.1 34540484 Porphyromonas gingivalis bphG BAA03892.1 425213 Pseudomonas sp adhE AAV66076.1 55818563 Leuconostoc mesenteroides Bld AAP42563.1 31075383 Clostridium saccharoperbutylacetonicum Ald ACL06658.1 218764192 Desulfatibacillum alkenivorans AK-01 Ald YP_001452373 157145054 Citrobacter koseri ATCC BAA-895 pduP NP_460996.1 16765381 Salmonella enterica Typhimurium pduP ABJ64680.1 116099531 Lactobacillus brevis ATCC 367 BselDRAFT_1651 ZP_02169447 163762382 Bacillus selenitireducens MLS10

An additional enzyme type that converts an acyl-CoA to its corresponding aldehyde is malonyl-CoA reductase which transforms malonyl-CoA to malonic semialdehyde. Malonyl-CoA reductase is a key enzyme in autotrophic carbon fixation via the 3-hydroxypropionate cycle in thermoacidophilic archaeal bacteria (Berg et al., Science 318:1782-1786 (2007); Thauer, Science 318:1732-1733 (2007)). The enzyme utilizes NADPH as a cofactor and has been characterized in Metallosphaera and Sulfolobus spp (Alber et al., J. Bacteriol. 188:8551-8559 (2006); Hugler et al., J. Bacteriol. 184:2404-2410(2002)). The enzyme is encoded by Msed_0709 in Metallosphaera sedula (Alber et al., supra (2006); Berg et al., Science 318:1782-1786 (2007)). A gene encoding a malonyl-CoA reductase from Sulfolobus tokodaii was cloned and heterologously expressed in E. coli (Alber et al., J. Bacteriol. 188:8551-8559 (2006)). This enzyme has also been shown to catalyze the conversion of methylmalonyl-CoA to its corresponding aldehyde (WO 2007/141208 (2007)). Although the aldehyde dehydrogenase functionality of these enzymes is similar to the bifunctional dehydrogenase from Chloroflexus aurantiacus, there is little sequence similarity. Both malonyl-CoA reductase enzyme candidates have high sequence similarity to aspartate-semialdehyde dehydrogenase, an enzyme catalyzing the reduction and concurrent dephosphorylation of aspartyl-4-phosphate to aspartate semialdehyde. Additional gene candidates can be found by sequence homology to proteins in other organisms including Sulfolobus solfataricus and Sulfolobus acidocaldarius and have been listed below. Yet another candidate for CoA-acylating aldehyde dehydrogenase is the ald gene from Clostridium beijerinckii (Toth et al., Appl. Environ. Microbiol. 65:4973-4980 (1999). This enzyme has been reported to reduce acetyl-CoA and butyryl-CoA to their corresponding aldehydes. This gene is very similar to eutE that encodes acetaldehyde dehydrogenase of Salmonella typhimurium and E. coli (Toth et al., supra). Such enzymes may be capable of naturally converting formyl-CoA to formaldehyde or can be engineered to do so.

Protein GenBank ID GI number Organism Msed_0709 YP_001190808.1 146303492 Metallosphaera sedula Mcr NP_378167.1 15922498 Sulfolobus tokodaii asd-2 NP_343563.1 15898958 Sulfolobus solfataricus Saci 2370 YP_256941.1 70608071 Sulfolobus acidocaldarius Ald AAT66436 9473535 Clostridium beijerinckii eutE AAA80209 687645 Salmonella typhimurium eutE P77445 2498347 Escherichia coli

Step H, FIG. 3: Formyltetrahydrofolate Synthetase

Formyltetrahydrofolate synthetase ligates formate to tetrahydrofolate at the expense of one ATP. This reaction is catalyzed by the gene product of Moth_0109 in M. thermoacetica (O'brien et al., Experientia Suppl. 26:249-262 (1976); Lovell et al., Arch. Microbiol. 149:280-285 (1988); Lovell et al., Biochemistry 29:5687-5694 (1990)), FHS in Clostridium acidurici (Whitehead and Rabinowitz, J. Bacteriol. 167:203-209 (1986); Whitehead and Rabinowitz, J Bacteriol. 170:3255-3261(1988), and CHY_2385 in C. hydrogenoformans (Wu et al., PLoS Genet. 1:e65 (2005). Homologs exist in C. carboxidivorans P7. This enzyme is found in several other organisms as listed below.

Protein GenBank ID GI number Organism Moth_0109 YP_428991.1 83588982 Moorella thermoacetica CHY_2385 YP_361182.1 78045024 Carboxydothermus hydrogenoformans FHS P13419.1 120562 Clostridium acidurici CcarbDRAFT_1913 ZP_05391913.1 255524966 Clostridium carboxidivorans P7 CcarbDRAFT_2946 ZP_05392946.1 255526022 Clostridium carboxidivorans P7 Dhaf_0555 ACL18622.1 219536883 Desulfitobacterium hafniense fhs YP_001393842.1 153953077 Clostridium kluyveri DSM 555 fhs YP_003781893.1 300856909 Clostridium ljungdahlii DSM 13528 MGA3_08300 EIJ83208.1 387590889 Bacillus methanolicus MGA3 PB1_13509 ZP_10132113.1 387929436 Bacillus methanolicus PB1

Steps I and J, FIG. 3: Formyltetrahydrofolate Synthetase and Methylenetetrahydrofolate Dehydrogenase

In M. thermoacetica, E. coli, and C. hydrogenoformans, methenyltetrahydrofolate cyclohydrolase and methylenetetrahydrofolate dehydrogenase are carried out by the bi-functional gene products of Moth_1516, folD, and CHY_1878, respectively (Pierce et al., Environ. Microbiol. 10:2550-2573 (2008); Wu et al., PLoS Genet. 1:e65 (2005); D'Ari and Rabinowitz, J Biol. Chem. 266:23953-23958 (1991)). A homolog exists in C. carboxidivorans P7. Several other organisms also encode for this bifunctional protein as tabulated below.

Protein GenBank ID GI number Organism Moth_1516 YP_430368.1 83590359 Moorella thermoacetica folD NP_415062.1 16128513 Escherichia coli CHY_1878 YP_360698.1 78044829 Carboxydothermus hydrogenoformans CcarbDRAFT_2948 ZP_05392948.1 255526024 Clostridium carboxidivorans P7 folD ADK16789.1 300437022 Clostridium ljungdahlii DSM 13528 folD-2 NP_951919.1 39995968 Geobacter sulfurreducens PCA folD YP_725874.1 113867385 Ralstonia eutropha H16 folD NP_348702.1 15895353 Clostridium acetobutylicum ATCC 824 folD YP_696506.1 110800457 Clostridium perfringens MGA3_09460 EIJ83438.1 387591119 Bacillus methanolicus MGA3 PB1_14689 ZP_10132349.1 387929672 Bacillus methanolicus PB1

Steps K, FIG. 3: Formaldehyde-Forming Enzyme or Spontaneous

Methylene-THF, or active formaldehyde, will spontaneously decompose to formaldehyde and THF (Thomdike and Beck, Cancer Res. 1977, 37(4) 1125-32; Ordonez and Caraballo, Psychopharmacol Commun. 1975 1(3) 253-60; Kallen and Jencks, 1966, J Biol Chem 241(24) 5851-63). To achieve higher rates, a formaldehyde-forming enzyme can be applied. Such an activity can be obtained by engineering an enzyme that reversibly forms methylene-THF from THF and a formaldehyde donor, to release free formaldehyde. Such enzymes include glycine cleavage system enzymes which naturally transfer a formaldehyde group from methylene-THF to glycine (see Step L, FIG. 3 for candidate enzymes). Additional enzymes include serine hydroxymethyltransferase (see Step M, FIG. 3 for candidate enzymes), dimethylglycine dehydrogenase (Porter, et al., Arch Biochem Biophys. 1985, 243(2) 396-407; Brizio et al., 2004, (37) 2, 434-442), sarcosine dehydrogenase (Porter, et al., Arch Biochem Biophys. 1985, 243(2) 396-407), and dimethylglycine oxidase (Leys, et al., 2003, The EMBO Journal 22(16) 4038-4048).

Protein GenBank ID GI number Organism dmgo ZP_09278452.1 359775109 Arthrobacter globiformis dmgo YP_002778684.1 226360906 Rhodococcus opacus B4 dmgo EFY87157.1 322695347 Metarhizium acridum CQMa 102 shd AAD53398.2 5902974 Homo sapiens shd NP_446116.1 GI: 25742657 Rattus norvegicus dmgdh NP_037523.2 24797151 Homo sapiens dmgdh Q63342.1 2498527 Rattus norvegicus

Step L, FIG. 3: Glycine Cleavage System

The reversible NAD(P)H-dependent conversion of 5,10-methylenetetrahydrofolate and CO₂ to glycine is catalyzed by the glycine cleavage complex, also called glycine cleavage system, composed of four protein components; P, H, T and L. The glycine cleavage complex is involved in glycine catabolism in organisms such as E. coli and glycine biosynthesis in eukaryotes (Kikuchi et al, Proc Jpn Acad Ser 84:246 (2008)). The glycine cleavage system of E. coli is encoded by four genes: gcvPHT and 1pdA (Okamura et al, Eur J Biochem 216:539-48 (1993); Heil et al, Microbiol 148:2203-14 (2002)). Activity of the glycine cleavage system in the direction of glycine biosynthesis has been demonstated in vivo in Saccharomyces cerevisiae (Maaheimo et al, Eur J Biochem 268:2464-79 (2001)). The yeast GCV is encoded by GCV1, GCV2, GCV3 and LPD1.

Protein GenBank ID GI Number Organism gcvP AAC75941.1 1789269 Escherichia coli gcvT AAC75943.1 1789272 Escherichia coli gcvH AAC75942.1 1789271 Escherichia coli lpdA AAC73227.1 1786307 Escherichia coli GCV1 NP_010302.1 6320222 Saccharomyces cerevisiae GCV2 NP_013914.1 6323843 Saccharomyces cerevisiae GCV3 NP_009355.3 269970294 Saccharomyces cerevisiae LPD1 NP_116635.1 14318501 Saccharomyces cerevisiae

Step M, FIG. 3: Serine Hydroxymethyltransferase

Conversion of glycine to serine is catalyzed by serine hydroxymethyltransferase, also called glycine hydroxymethyltranferase. This enzyme reversibly converts glycine and 5,10-methylenetetrahydrofolate to serine and THF. Serine methyltransferase has several side reactions including the reversible cleavage of 3-hydroxyacids to glycine and an aldehyde, and the hydrolysis of 5,10-methenyl-THF to 5-formyl-THF. This enzyme is encoded by glyA of E. coli (Plamann et al, Gene 22:9-18 (1983)). Serine hydroxymethyltranferase enzymes of S. cerevisiae include SHM1 (mitochondrial) and SHM2 (cytosolic) (McNeil et al, J Biol Chem 269:9155-65 (1994)). Similar enzymes have been studied in Corynebacterium glutamicum and Methylobacterium extorquens (Chistoserdova et al, J. Bacteriol 176:6759-62 (1994); Schweitzer et al, J Biotechnol 139:214-21(2009)).

Protein GenBank ID GI Number Organism glyA AAC75604.1 1788902 Escherichia coli SHM1 NP_009822.2 37362622 Saccharomyces cerevisiae SHM2 NP_013159.1 6323087 Saccharomyces cerevisiae glyA AAA64456.1 496116 Methylobacterium extorquens glyA AAK60516.1 14334055 Corynebacterium glutamicum

Step N, FIG. 3: Serine Deaminase

Serine can be deaminated to pyruvate by serine deaminase. Serine deaminase enzymes are present in several organisms including Clostridium acidurici (Carter, et al., 1972, J. Bacteriol., 109(2) 757-763), Escherichia coli (Cicchillo et al., 2004, J Biol Chem., 279(31) 32418-25), and Corneybacterium sp. (Netzer et al., Appl Environ Microbiol. 2004 December; 70(12):7148-55).

Protein GenBank ID GI Number Organism sdaA YP_490075.1 388477887 Escherichia coli sdaB YP_491005.1 388478813 Escherichia coli tdcG YP_491301.1 388479109 Escherichia coli tdcB YP_491307.1 388479115 Escherichia coli sdaA YP_225930.1 62390528 Corynebacterium sp.

Step O, FIG. 3: Methylenetetrahydrofolate Reductase

In M. thermoacetica, this enzyme is oxygen-sensitive and contains an iron-sulfur cluster (Clark and Ljungdahl, J Biol. Chem. 259:10845-10849 (1984). This enzyme is encoded by metF in E. coli (Sheppard et al., J. Bacteriol. 181:718-725 (1999) and CHY_1233 in C. hydrogenoformans (Wu et al., PLoS Genet. 1:e65 (2005). The M. thermoacetica genes, and its C. hydrogenoformans counterpart, are located near the CODH/ACS gene cluster, separated by putative hydrogenase and heterodisulfide reductase genes. Some additional gene candidates found bioinformatically are listed below. In Acetobacterium woodii metF is coupled to the Rnf complex through RnfC2 (Poehlein et al, PLoS One. 7:e33439). Homologs of RnfC are found in other organisms by blast search. The Rnf complex is known to be a reversible complex (Fuchs (2011) Annu. Rev. Microbiol. 65:631-658).

Protein GenBank ID GI number Organism Moth_1191 YP_430048.1 83590039 Moorella thermoacetica Moth_1192 YP_430049.1 83590040 Moorella thermoacetica metF NP_418376.1 16131779 Escherichia coli CHY_1233 YP_360071.1 78044792 Carboxydothermus hydrogenoformans CLJU_c37610 YP_003781889.1 300856905 Clostridium ljungdahlii DSM 13528 DesfrDRAFT_3717 ZP_07335241.1 303248996 Desulfovibrio fructosovorans JJ CcarbDRAFT_2950 ZP_05392950.1 255526026 Clostridium carboxidivoransP7 Ccel74_010100023124 ZP_07633513.1 307691067 Clostridium cellulovorans 743B Cphy_3110 YP_001560205.1 160881237 Clostridium phytofermentans ISDg

Step P, FIG. 3: Acetyl-CoA Synthase

Acetyl-CoA synthase is the central enzyme of the carbonyl branch of the Wood-Ljungdahl pathway. It catalyzes the synthesis of acetyl-CoA from carbon monoxide, coenzyme A, and the methyl group from a methylated corrinoid-iron-sulfur protein. The corrinoid-iron-sulfur-protein is methylated by methyltetrahydrofolate via a methyltransferase. Expression in a foreign host entails introducing one or more of the following proteins and their corresponding activities: Methyltetrahydrofolate:corrinoid protein methyltransferase (AcsE), Corrinoid iron-sulfur protein (AcsD), Nickel-protein assembly protein (AcsF), Ferredoxin (Orf7), Acetyl-CoA synthase (AcsB and AcsC), Carbon monoxide dehydrogenase (AcsA), and Nickel-protein assembly protein (CooC).

The genes used for carbon-monoxide dehydrogenase/acetyl-CoA synthase activity typically reside in a limited region of the native genome that can be an extended operon (Ragsdale, S. W., Crit. Rev. Biochem. Mol. Biol. 39:165-195 (2004); Morton et al., J. Biol. Chem. 266:23824-23828 (1991); Roberts et al., Proc. Nat. Acad Sci. USA. 86:32-36 (1989). Each of the genes in this operon from the acetogen, M. thermoacetica, has already been cloned and expressed actively in E. coli (Morton et al. supra; Roberts et al. supra; Lu et al., J Biol. Chem. 268:5605-5614 (1993). The protein sequences of these genes can be identified by the following GenBank accession numbers.

Protein GenBank ID GI number Organism AcsE YP_430054 83590045 Moorella thermoacetica AcsD YP_430055 83590046 Moorella thermoacetica AcsF YP_430056 83590047 Moorella thermoacetica Orf7 YP_430057 83590048 Moorella thermoacetica AcsC YP_430058 83590049 Moorella thermoacetica AcsB YP_430059 83590050 Moorella thermoacetica AcsA YP_430060 83590051 Moorella thermoacetica CooC YP_430061 83590052 Moorella thermoacetica

The hydrogenic bacterium, Carboxydothermus hydrogenoformans, can utilize carbon monoxide as a growth substrate by means of acetyl-CoA synthase (Wu et al., PLoS Genet. 1:e65 (2005)). In strain Z-2901, the acetyl-CoA synthase enzyme complex lacks carbon monoxide dehydrogenase due to a frameshift mutation (Wu et al. supra (2005)), whereas in strain DSM 6008, a functional unframeshifted full-length version of this protein has been purified (Svetlitchnyi et al., Proc. Nat. Acad. Sci. USA. 101:446-451(2004)). The protein sequences of the C. hydrogenoformans genes from strain Z-2901 can be identified by the following GenBank accession numbers.

Protein GenBank ID GI number Organism AcsE YP_360065 78044202 Carboxydothermus hydrogenoformans AcsD YP_360064 78042962 Carboxydothermus hydrogenoformans AcsF YP_360063 78044060 Carboxydothermus hydrogenoformans Orf7 YP_360062 78044449 Carboxydothermus hydrogenoformans AcsC YP_360061 78043584 Carboxydothermus hydrogenoformans AcsB YP_360060 78042742 Carboxydothermus hydrogenoformans CooC YP_360059 78044249 Carboxydothermus hydrogenoformans

Homologous ACS/CODH genes can also be found in the draft genome assembly of Clostridium carboxidivorans P7.

Protein GenBank ID GI Number Organism AcsA ZP_05392944.1 255526020 Clostridium carboxidivorans P7 CooC ZP_05392945.1 255526021 Clostridium carboxidivorans P7 AcsF ZP_05392952.1 255526028 Clostridium carboxidivorans P7 AcsD ZP_05392953.1 255526029 Clostridium carboxidivorans P7 AcsC ZP_05392954.1 255526030 Clostridium carboxidivorans P7 AcsE ZP_05392955.1 255526031 Clostridium carboxidivorans P7 AcsB ZP_05392956.1 255526032 Clostridium carboxidivorans P7 Orf7 ZP_05392958.1 255526034 Clostridium carboxidivorans P7

The methanogenic archaeon, Methanosarcina acetivorans, can also grow on carbon monoxide, exhibits acetyl-CoA synthase/carbon monoxide dehydrogenase activity, and produces both acetate and formate (Lessner et al., Proc. Natl. Acad. Sci. USA. 103:17921-17926 (2006)). This organism contains two sets of genes that encode ACS/CODH activity (Rother and Metcalf, Proc. Natl. Acad. Sci. USA. 101:16929-16934 (2004)). The protein sequences of both sets of M. acetivorans genes are identified by the following GenBank accession numbers.

Protein GenBank ID GI number Organism AcsC NP_618736 20092661 Methanosarcina acetivorans AcsD NP_618735 20092660 Methanosarcina acetivorans AcsF, CooC NP_618734 20092659 Methanosarcina acetivorans AcsB NP_618733 20092658 Methanosarcina acetivorans AcsEps NP_618732 20092657 Methanosarcina acetivorans AcsA NP_618731 20092656 Methanosarcina acetivorans AcsC NP_615961 20089886 Methanosarcina acetivorans AcsD NP_615962 20089887 Methanosarcina acetivorans AcsF, CooC NP_615963 20089888 Methanosarcina acetivorans AcsB NP_615964 20089889 Methanosarcina acetivorans AcsEps NP_615965 20089890 Methanosarcina acetivorans AcsA NP_615966 20089891 Methanosarcina acetivorans

The AcsC, AcsD, AcsB, AcsEps, and AcsA proteins are commonly referred to as the gamma, delta, beta, epsilon, and alpha subunits of the methanogenic CODH/ACS. Homologs to the epsilon encoding genes are not present in acetogens such as M. thermoacetica or hydrogenogenic bacteria such as C. hydrogenoformans. Hypotheses for the existence of two active CODH/ACS operons in M. acetivorans include catalytic properties (i.e., K_(m), V_(max), k_(cat)) that favor carboxidotrophic or aceticlastic growth or differential gene regulation enabling various stimuli to induce CODH/ACS expression (Rother et al., Arch. Microbiol. 188:463-472 (2007)).

Step Y, FIG. 3: Glyceraldehydes-3-Phosphate Dehydrogenase and Enzymes of Lower Glycolysis

Enzymes comprising Step Y, G31P to PYR include: Glyceraldehyde-3-phosphate dehydrogenase; Phosphoglycerate kinase; Phosphoglyceromutase; Enolase; Pyruvate kinase or PTS-dependent substrate import.

Glyceraldehyde-3-phosphate dehydrogenase enzymes include:

NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, exemplary enzymes are:

Protein GenBank ID GI Number Organism gapN AAA91091.1 642667 Streptococcus mutans NP-GAPDH AEC07555.1 330252461 Arabidopsis thaliana GAPN AAM77679.2 82469904 Triticum aestivum gapN CAI56300.1 87298962 Clostridium acetobutylicum NADP-GAPDH 2D2I_A 112490271 Synechococcus elongatus PCC 7942 NADP-GAPDH CAA62619.1 4741714 Synechococcus elongatus PCC 7942 GDP1 XP_455496.1 50310947 Kluyveromyces lactis NRRL Y-1140 HP1346 NP_208138.1 15645959 Helicobacter pylori 26695 and NAD-dependent glyceraldehyde-3-phosphate dehydrogenase, exemplary enzymes are:

Protein GenBank ID GI Number Organism TDH1 NP_012483.1 6322409 Saccharomyces cerevisiae s288c TDH2 NP_012542.1 6322468 Saccharomyces cerevisiae s288c TDH3 NP_011708.1 632163 Saccharomyces cerevisiae s288c KLLA0A11858g XP_451516.1 50303157 Kluyveromyces lactis NRRL Y-1140 KLLA0F20988g XP_456022.1 50311981 Kluyveromyces lactis NRRL Y-1140 ANI_1_256144 XP_001397496.1 145251966 Aspergillus niger CBS 513.88 YALI0C06369g XP_501515.1 50548091 Yarrowia lipolytica CTRG_05666 XP_002551368.1 255732890 Candida tropicalis MYA-3404 HPODL_1089 EFW97311.1 320583095 Hansenula polymorpha DL-1 gapA YP_490040.1 388477852 Escherichia coli Phosphoglycerate kinase enzymes include:

Protein GenBank ID GI Number Organism PGK1 NP_009938.2 10383781 Saccharomyces cerevisiae s288c PGK BAD83658.1 57157302 Candida boidinii PGK EFW98395.1 320584184 Hansenula polymorpha DL-1 pgk EIJ77825.1 387585500 Bacillus methanolicus MGA3 pgk YP_491126.1 388478934 Escherichia coli Phosphoglyceromutase (aka phosphoglycerate mutase) enzymes include;

Protein GenBank ID GI Number Organism GPM1 NP_012770.1 6322697 Saccharomyces cerevisiae s288c GPM2 NP_010263.1 6320183 Saccharomyces cerevisiae s288c GPM3 NP_014585.1 6324516 Saccharomyces cerevisiae s288c HPODL 1391 EFW96681.1 320582464 Hansenula polymorpha DL-1 HPODL_0376 EFW97746.1 320583533 Hansenula polymorpha DL-1 gpmI EIJ77827.1 387585502 Bacillus methanolicus MGA3 gpmA YP_489028.1 388476840 Escherichia coli gpmM AAC76636.1 1790041 Escherichia coli Enolase (also known as phosphopyruvate hydratase and 2-phosphoglycerate dehydratase) enzymes include:

Protein GenBank ID GI Number Organism ENO1 NP_011770.3 398366315 Saccharomyces cerevisiae s288c ENO2 AAB68019.1 458897 Saccharomyces cerevisiae s288c HPODL_2596 EFW95743.1 320581523 Hansenula polymorpha DL-1 eno EIJ77828.1 387585503 Bacillus methanolicus MGA3 eno AAC75821.1 1789141 Escherichia coli

Pyruvate kinase (also known as phosphoenolpyruvate kinase and phosphoenolpyruvate kinase) or PTS-dependent substrate import enzymes include those below. Pyruvate kinase, also known as phosphoenolpyruvate synthase (EC 2.7.9.2), converts pyruvate and ATP to PEP and AMP. This enzyme is encoded by the PYK1 (Burke et al., J. Biol. Chem. 258:2193-2201(1983)) and PYK2 (Boles et al., J. Bacteriol. 179:2987-2993 (1997)) genes in S. cerevisiae. In E. coli, this activity is catalyzed by the gene products of pykF and pykA. Note that pykA and pykF are genes encoding separate enzymes potentially capable of carrying out the PYK reaction. Selected homologs of the S. cerevisiae enzymes are also shown in the table below.

Protein GenBank ID GI Number Organism PYK1 XP_009362 6319279 Saccharomyces cerevisiae PYK2 XP_014992 6324923 Saccharomyces cerevisiae pykF XP_416191.1 16129632 Escherichia coli pykA XP_416368.1 16129807 Escherichia coli KLLA0F23397g XP_456122.1 50312181 Kluyveromyces lactis CaO19.3575 XP_714934.1 68482353 Candida albicans CaO19.11059 XP_714997.1 68482226 Candida albicans YALI0F09185p XP_505195 210075987 Yarrowia lipolytica ANI_1_1126064 XP_001391973 145238652 Aspergillus niger MGA3_03005 EIJ84220.1 387591903 Bacillus methanolicus MGA3 HPODL_1539 EFW96829.1 320582612 Hansenula polymorpha DL-1

PTS-dependent substrate uptake systems catalyze a phosphotransfer cascade that couples conversion of PEP to pyruvate with the transport and phosphorylation of carbon substrates. For example, the glucose PTS system transports glucose, releasing glucose-6-phosphate into the cytoplasm and concomitantly converting phosphoenolpyruvate to pyruvate. PTS systems are comprised of substrate-specific and non-substrate-specific components. In E. coli the two non-specific components are encoded by ptsI (Enzyme I) and ptsH (HPr). The sugar-dependent components are encoded by crr and ptsG. Pts systems have been extensively studied and are reviewed, for example in Postma et al, Microbiol Rev 57: 543-94 (1993).

Protein GenBank ID GI Number Organism ptsG AC74185.1 1787343 Escherichia coli ptsI AAC75469.1 1788756 Escherichia coli ptsH AAC75468.1 1788755 Escherichia coli crr AAC75470.1 1788757 Escherichia coli

The IIA[Glc] component mediates the transfer of the phosphoryl group from histidine protein Hpr (ptsH) to the IIB[Glc] (ptsG) component. A truncated variant of the crr gene was introduced into 1,4-butanediol producing strains.

Alternatively, Phosphoenolpyruvate phosphatase (EC 3.1.3.60) catalyzes the hydrolysis of PEP to pyruvate and phosphate. Numerous phosphatase enzymes catalyze this activity, including alkaline phosphatase (EC 3.1.3.1), acid phosphatase (EC 3.1.3.2), phosphoglycerate phosphatase (EC 3.1.3.20) and PEP phosphatase (EC 3.1.3.60). PEP phosphatase enzymes have been characterized in plants such as Vignia radiate, Bruguiera sexangula and Brassica nigra. The phytase from Aspergillus fumigates, the acid phosphatase from Homo sapiens and the alkaline phosphatase of E. coli also catalyze the hydrolysis of PEP to pyruvate (Brugger et al, Appl Microbiol Biotech 63:383-9 (2004); Hayman et al, Biochem J 261:601-9 (1989); et al, The Enzymes 3rd Ed. 4:373-415 (1971))). Similar enzymes have been characterized in Campylobacter jejuni (van Mourik et al., Microbiol. 154:584-92 (2008)), Saccharomyces cerevisiae (Oshima et al., Gene 179:171-7 (1996)) and Staphylococcus aureus (Shah and Blobel, J. Bacteriol. 94:780-1(1967)). Enzyme engineering and/or removal of targeting sequences may be required for alkaline phosphatase enzymes to function in the cytoplasm.

Protein GenBank ID GI Number Organism phyA O00092.1 41017447 Aspergillus fumigatus Acp5 P13686.3 56757583 Homo sapiens phoA XP_414917.2 49176017 Escherichia coli phoX ZP_01072054.1 86153851 Campylobacter jejuni PHO8 AAA34871.1 172164 Saccharomyces cerevisiae SaurJH1_2706 YP_001317815.1 150395140 Staphylococcus aureus

Step Q, FIG. 3: Pyruvate Formate Lyase

Pyruvate formate-lyase (PFL, EC 2.3.1.54), encoded by pflB in E. coli, can convert pyruvate into acetyl-CoA and formate. The activity of PFL can be enhanced by an activating enzyme encoded by pflA (Knappe et al., Proc. Natl. Acad. Sci USA 81:1332-1335 (1984); Wong et al., Biochemistry 32:14102-14110 (1993)). Keto-acid formate-lyase (EC 2.3.1.-), also known as 2-ketobutyrate formate-lyase (KFL) and pyruvate formate-lyase 4, is the gene product of tdcE in E. coli. This enzyme catalyzes the conversion of 2-ketobutyrate to propionyl-CoA and formate during anaerobic threonine degradation, and can also substitute for pyruvate formate-lyase in anaerobic catabolism (Simanshu et al., J Biosci. 32:1195-1206 (2007)). The enzyme is oxygen-sensitive and, like PflB, can require post-translational modification by PFL-AE to activate a glycyl radical in the active site (Hesslinger et al., Mol. Microbiol 27:477-492 (1998)). A pyruvate formate-lyase from Archaeglubus fulgidus encoded by pflD has been cloned, expressed in E. coli and characterized (Lehtio et al., Protein Eng Des Sel 17:545-552 (2004)). The crystal structures of the A. fulgidus and E. coli enzymes have been resolved (Lehtio et al., J Mol. Biol. 357:221-235 (2006); Leppanen et al., Structure. 7:733-744 (1999)). Additional PFL and PFL-AE candidates are found in Lactococcus lactis (Melchiorsen et al., Appl Microbiol Biotechnol 58:338-344 (2002)), and Streptococcus mutans (Takahashi-Abbe et al., Oral. Microbiol Immunol. 18:293-297 (2003)), Chlamydomonas reinhardtii (Hemschemeier et al., Eukaryot. Cell 7:518-526 (2008b); Atteia et al., J Biol. Chem. 281:9909-9918 (2006)) and Clostridium pasteurianum (Weidner et al., J. Bacteriol. 178:2440-2444 (1996)).

Protein GenBank ID GI Number Organism pflB XP_415423 16128870 Escherichia coli pflA NP_415422.1 16128869 Escherichia coli tdcE AAT48170.1 48994926 Escherichia coli pflD XP_070278.1 11499044 Archaeglubus fulgidus Pfl CAA03993 2407931 Lactococcus lactis Pfl BAA09085 1129082 Streptococcus mutans PFL1 XP_001689719.1 159462978 Chlamydomonas reinhardtii pflA1 XP_001700657.1 159485246 Chlamydomonas reinhardtii Pfl Q46266.1 2500058 Clostridium pasteurianum Act CAA63749.1 1072362 Clostridium pasteurianum

Step R, FIG. 3: Pyruvate Dehydrogenase, Pyruvate Ferredoxin Oxidoreductase, Pyruvate:NADP+ Oxidoreductase

The pyruvate dehydrogenase (PDH) complex catalyzes the conversion of pyruvate to acetyl-CoA (FIG. 3R). The E. coli PDH complex is encoded by the genes aceEF and 1pdA. Enzyme engineering efforts have improved the E. coli PDH enzyme activity under anaerobic conditions (Kim et al., J. Bacteriol. 190:3851-3858 (2008); Kim et al., Appl. Environ. Microbiol. 73:1766-1771(2007); Zhou et al., Biotechnol. Lett. 30:335-342 (2008)). In contrast to the E. coli the B. subtilis complex is active and required for growth under anaerobic conditions (Nakano et al., 179:6749-6755 (1997)). The Klebsiella pneumoniae PDH, characterized during growth on glycerol, is also active under anaerobic conditions (Menzel et al., 56:135-142 (1997)). Crystal structures of the enzyme complex from bovine kidney (Zhou et al., 98:14802-14807 (2001)) and the E2 catalytic domain from Azotobacter vinelandii are available (Mattevi et al., Science. 255:1544-1550 (1992)). Some mammalian PDH enzymes complexes can react on alternate substrates such as 2-oxobutanoate. Comparative kinetics of Rattus norvegicus PDH and BCKAD indicate that BCKAD has higher activity on 2-oxobutanoate as a substrate (Paxton et al., Biochem. J. 234:295-303 (1986)). The S. cerevisiae PDH complex can consist of an E2 (LAT1) core that binds E1 (PDA1, PDB1), E3(LPD1), and Protein X (PDX1) components (Pronk et al., Yeast 12:1607-1633(1996)). The PDH complex of S. cerevisiae is regulated by phosphorylation of E1 involving PKP1 (PDH kinase I), PTC5 (PDH phosphatase I), PKP2 and PTC6. Modification of these regulators may also enhance PDH activity. Coexpression of lipoyl ligase (LplA of E. coli and AM22 in S. cerevisiae) with PDH in the cytosol may be necessary for activating the PDH enzyme complex. Increasing the supply of cytosolic lipoate, either by modifying a metabolic pathway or media supplementation with lipoate, may also improve PDH activity.

Gene Accession No. GI Number Organism aceE XP_414656.1 16128107 Escherichia coli aceF NP_414657.1 16128108 Escherichia coli lpd XP_414658.1 16128109 Escherichia coli lplA XP_418803.1 16132203 Escherichia coli pdhA P21881.1 3123238 Bacillus subtilis pdhB P21882.1 129068 Bacillus subtilis pdhC P21883.2 129054 Bacillus subtilis pdhD P21880.1 118672 Bacillus subtilis aceE YP_001333808.1 152968699 Klebsiella pneumoniae aceF YP_001333809.1 152968700 Klebsiella pneumoniae lpdA YP_001333810.1 152968701 Klebsiella pneumoniae Pdha1 XP_001004072.2 124430510 Rattus norvegicus Pdha2 XP_446446.1 16758900 Rattus norvegicus Dlat NP_112287.1 78365255 Rattus norvegicus Dld XP_955417.1 40786469 Rattus norvegicus LAT1 NP_014328 6324258 Saccharomyces cerevisiae PDA1 XP_011105 37362644 Saccharomyces cerevisiae PDB1 NP_009780 6319698 Saccharomyces cerevisiae LPD1 XP_116635 14318501 Saccharomyces cerevisiae PDX1 NP_011709 6321632 Saccharomyces cerevisiae AIM22 NP_012489.2 83578101 Saccharomyces cerevisiae

As an alternative to the large multienzyme PDH complexes described above, some organisms utilize enzymes in the 2-ketoacid oxidoreductase family (OFOR) to catalyze acylating oxidative decarboxylation of 2-keto-acids. Unlike the PDH complexes, PFOR enzymes contain iron-sulfur clusters, utilize different cofactors and use ferredoxin or flavodixin as electron acceptors in lieu of NAD(P)H. Pyruvate ferredoxin oxidoreductase (PFOR) can catalyze the oxidation of pyruvate to formacetyl-CoA (FIG. 3R). The PFOR from Desulfovibrio africanus has been cloned and expressed in E. coli resulting in an active recombinant enzyme that was stable for several days in the presence of oxygen (Pieulle et al., J. Bacteriol. 179:5684-5692 (1997)). Oxygen stability is relatively uncommon in PFORs and is believed to be conferred by a 60 residue extension in the polypeptide chain of the D. africanus enzyme. The M. thermoacetica PFOR is also well characterized (Menon et al., Biochemistry 36:8484-8494 (1997)) and was even shown to have high activity in the direction of pyruvate synthesis during autotrophic growth (Furdui et al., J Biol Chem. 275:28494-28499 (2000)). Further, E. coli possesses an uncharacterized open reading frame, ydbK, that encodes a protein that is 51% identical to the M. thermoacetica PFOR Evidence for pyruvate oxidoreductase activity in E. coli has been described (Blaschkowski et al., Eur. J Biochem. 123:563-569 (1982)). Several additional PFOR enzymes are described in Ragsdale, Chem. Rev. 103:2333-2346 (2003). Finally, flavodoxin reductases (e.g., fqrB from Helicobacter pylori or Campylobacter jejuni (St Maurice et al., J. Bacteriol. 189:4764-4773 (2007))) or Rnf-type proteins (Seedorf et al., Proc. Natl. Acad Sci. USA. 105:2128-2133 (2008); Herrmann et al., J. Bacteriol. 190:784-791(2008)) provide a means to generate NADH or NADPH from the reduced ferredoxin generated by PFOR These proteins are identified below.

Protein GenBank ID GI Number Organism Por CAA70873.1 1770208 Desulfovibrio africanus Por YP_428946.1 83588937 Moorella thermoacetica ydbK NP_415896.1 16129339 Escherichia coli fqrB XP_207955.1 15645778 Helicobacter pylori fqrB YP_001482096.1 157414840 Campylobacter jejuni RnfC EDK33306.1 146346770 Clostridium kluyveri RnfD EDK33307.1 146346771 Clostridium kluyveri RnfG EDK33308.1 146346772 Clostridium kluyveri RnfE EDK33309.1 146346773 Clostridium kluyveri RnfA EDK33310.1 146346774 Clostridium kluyveri RnfB EDK33311.1 146346775 Clostridium kluyveri

Pyruvate:NADP oxidoreductase (PNO) catalyzes the conversion of pyruvate to acetyl-CoA. This enzyme is encoded by a single gene and the active enzyme is a homodimer, in contrast to the multi-subunit PDH enzyme complexes described above. The enzyme from Euglena gracilsis stabilized by its cofactor, thiamin pyrophosphate (Nakazawa et al, Arch Biochem Biophys 411:183-8 (2003)). The mitochondrial targeting sequence of this enzyme should be removed for expression in the cytosol. The PNO protein of E. gracilis and other NADP-dependent pyruvate:NADP+ oxidoreductase enzymes are listed in the table below.

Protein GenBank ID GI Number Organism PNO Q94IN5.1 33112418 Euglena gracilis cgd4_690 XP_625673.1 66356990 Cryptosporidium parvum Iowa II TPP_PFOR_PNO XP_002765111.11 294867463 Perkinsus marinus ATCC 50983

Step S, FIG. 3: Formate Dehydrogenase

Formate dehydrogenase (FDH) catalyzes the reversible transfer of electrons from formate to an acceptor. Enzymes with FDH activity utilize various electron carriers such as, for example, NADH (EC 1.2.1.2), NADPH (EC 1.2.1.43), quinols (EC 1.1.5.6), cytochromes (EC 1.2.2.3) and hydrogenases (EC 1.1.99.33). FDH enzymes have been characterized from Moorella thermoacetica (Andreesen and Ljungdahl, J. Bacteriol 116:867-873 (1973); Li et al., J Bacteriol 92:405-412 (1966); Yamamoto et al., J Biol Chem. 258:1826-1832 (1983). The loci, Moth_2312 is responsible for encoding the alpha subunit of formate dehydrogenase while the beta subunit is encoded by Moth_2314 (Pierce et al., Environ Microbiol (2008)). Another set of genes encoding formate dehydrogenase activity with a propensity for CO₂ reduction is encoded by Sfum_2703 through Sfum_2706 in Syntrophobacter fumaroxidans (de Bok et al., Eur J Biochem. 270:2476-2485 (2003)); Reda et al., PNAS 105:10654-10658 (2008)). A similar set of genes presumed to carry out the same function are encoded by CHY_0731, CHY_0732, and CHY_0733 in C. hydrogenoformans (Wu et al., PLoS Genet 1:e65 (2005)). Formate dehydrogenases are also found many additional organisms including C. carboxidivorans P7, Bacillus methanolicus, Burkholderia stabilis, Moorella thermoacetica ATCC 39073, Candida boidinii, Candida methylica, and Saccharomyces cerevisiae S288c. The soluble formate dehydrogenase from Ralstonia eutropha reduces NAD+(fdsG, -B, -A, -C, -D) (Oh and Bowien, 1998)

Several EM8 enzymes have been identified that have higher specificity for NADP as the cofactor as compared to NAD. This enzyme has been deemed as the NADP-dependent formate dehydrogenase and has been reported from 5 species of the Burkholderia cepacia complex. It was tested and verified in multiple strains of Burkholderia multivorans, Burkholderia stabilis, Burkholderia pyrrocinia, and Burkholderia cenocepacia (Hatrongjit et al., Enzyme and Microbial Tech., 46: 557-561(2010)). The enzyme from Burkholderia stabilis has been characterized and the apparent K_(m) of the enzyme were reported to be 55.5 mM, 0.16 mM and 1.43 mM for formate, NADP, and NAD respectively. More gene candidates can be identified using sequence homology of proteins deposited in Public databases such as NCBI, JGI and the metagenomic databases.

Protein GenBank ID GI Number Organism Moth_2312 YP_431142 148283121 Moorella thermoacetica Moth_2314 YP_431144 83591135 Moorella thermoacetica Sfum_2703 YP_846816.1 116750129 Syntrophobacter fumaroxidans Sfum_2704 YP_846817.1 116750130 Syntrophobacter fumaroxidans Sfum_2705 YP_846818.1 116750131 Syntrophobacter fumaroxidans Sfum_2706 YP_846819.1 116750132 Syntrophobacter fumaroxidans CHY_0731 YP_359585.1 78044572 Carboxydothermus hydrogenoformans CHY_0732 YP_359586.1 78044500 Carboxydothermus hydrogenoformans CHY_0733 YP_359587.1 78044647 Carboxydothermus hydrogenoformans CcarbDRAFT_0901 ZP_05390901.1 255523938 Clostridium carboxidivorans P7 CcarbDRAFT_4380 ZP_05394380.1 255527512 Clostridium carboxidivorans P7 fdhA, MGA3_06625 EIJ82879.1 387590560 Bacillus methanolicus MGA3 fdhA, PB1_11719 ZP_10131761.1 387929084 Bacillus methanolicus PB1 fdhD, MGA3_06630 EIJ82880.1 387590561 Bacillus methanolicus MGA3 fdhD, PB1_11724 ZP_10131762.1 387929085 Bacillus methanolicus PB1 fdh ACF35003.1 194220249 Burkholderia stabilis fdh ACF35004.1 194220251 Burkholderia pyrrocinia fdh ACF35002.1 194220247 Burkholderia cenocepacia fdh ACF35001.1 194220245 Burkholderia multivorans fdh ACF35000.1 194220243 Burkholderia cepacia FDH1 AAC49766.1 2276465 Candida boidinii fdh CAA57036.1 1181204 Candida methylica FDH2 P0CF35.1 294956522 Saccharomyces cerevisiae S288c FDH1 NP_015033.1 6324964 Saccharomyces cerevisiae S288c fdsG YP_725156.1 113866667 Ralstonia eutropha fdsB YP_725157.1 113866668 Ralstonia eutropha fdsA YP_725158.1 113866669 Ralstonia eutropha fdsC YP_725159.1 113866670 Ralstonia eutropha fdsD YP_725160.1 113866671 Ralstonia eutropha

Example IV Production of Reducing Equivalents and Formaldehyde from Methonal

This example describes methanol metabolic pathways and other additional enzymes for generating reducing equivalents as shown in FIG. 4 and for production of formaldehyde as shown in FIG. 3.

FIG. 4, Step a—Methanol Methyltransferase

A complex of 3-methyltransferase proteins, denoted MtaA, MtaB, and MtaC, perform the desired methanol methyltransferase activity (Sauer et al., Eur. J Biochem. 243:670-677 (1997); Naidu and Ragsdale, J. Bacteriol. 183:3276-3281(2001); Tallant and Krzycki, J Biol. Chem. 276:4485-4493 (2001); Tallant and Krzycki, J. Bacteriol. 179:6902-6911(1997); Tallant and Krzycki, J. Bacteriol. 178:1295-1301 (1996); Ragsdale, S. W., Crit. Rev. Biochem. Mol. Biol. 39:165-195 (2004)).

MtaB is a zinc protein that can catalyze the transfer of a methyl group from methanol to MtaC, a corrinoid protein. Exemplary genes encoding MtaB and MtaC can be found in methanogenic archaea such as Methanosarcina barkeri (Maeder et al., J. Bacteriol. 188:7922-7931(2006) and Methanosarcina acetivorans (Galagan et al., Genome Res. 12:532-542 (2002), as well as the acetogen, Moorella thermoacetica (Das et al., Proteins 67:167-176 (2007). In general, the MtaB and MtaC genes are adjacent to one another on the chromosome as their activities are tightly interdependent. The protein sequences of various MtaB and MtaC encoding genes in M. barkeri, M. acetivorans, and M. thermoaceticum can be identified by their following GenBank accession numbers.

Protein GenBank ID GI number Organism MtaB1 YP_304299 73668284 Methanosarcina barkeri MtaC1 YP_304298 73668283 Methanosarcina barkeri MtaB2 YP_307082 73671067 Methanosarcina barkeri MtaC2 YP_307081 73671066 Methanosarcina barkeri MtaB3 YP_304612 73668597 Methanosarcina barkeri MtaC3 YP_304611 73668596 Methanosarcina barkeri MtaB1 NP_615421 20089346 Methanosarcina acetivorans MtaB1 NP_615422 20089347 Methanosarcina acetivorans MtaB2 NP_619254 20093179 Methanosarcina acetivorans MtaC2 NP_619253 20093178 Methanosarcina acetivorans MtaB3 NP_616549 20090474 Methanosarcina acetivorans MtaC3 NP_616550 20090475 Methanosarcina acetivorans MtaB YP_430066 83590057 Moorella thermoacetica MtaC YP_430065 83590056 Moorella thermoacetica MtaA YP_430064 83590056 Moorella thermoacetica

The MtaB1 and MtaC1 genes, YP_304299 and YP_304298, from M. barkeri were cloned into E. coli and sequenced (Sauer et al., Eur. J Biochem. 243:670-677 (1997)). The crystal structure of this methanol-cobalamin methyltransferase complex is also available (Hagemeier et al., Proc. Nat. Acad Sci. USA. 103:18917-18922 (2006)). The MtaB genes, YP_307082 and YP_304612, in M. barkeri were identified by sequence homology to YP_304299. In general, homology searches are an effective means of identifying methanol methyltransferases because MtaB encoding genes show little or no similarity to methyltransferases that act on alternative substrates such as trimethylamine, dimethylamine, monomethylamine, or dimethylsulfide. The MtaC genes, YP_307081 and YP_304611 were identified based on their proximity to the MtaB genes and also their homology to YP_304298. The three sets of MtaB and MtaC genes from M. acetivorans have been genetically, physiologically, and biochemically characterized (Pritchett and Metcaf, Mol. Microbiol. 56:1183-1194 (2005)). Mutant strains lacking two of the sets were able to grow on methanol, whereas a strain lacking all three sets of MtaB and MtaC genes sets could not grow on methanol. This suggests that each set of genes plays a role in methanol utilization. The M. thermoacetica MtaB gene was identified based on homology to the methanogenic MtaB genes and also by its adjacent chromosomal proximity to the methanol-induced corrinoid protein, MtaC, which has been crystallized (Zhou et al., Acta Crystallogr. Sect. F Struct. Biol. Cyrst. Commun. 61:537-540 (2005) and further characterized by Northern hybridization and Western Blotting ((Das et al., Proteins 67:167-176 (2007)).

MtaA is zinc protein that catalyzes the transfer of the methyl group from MtaC to either Coenzyme M in methanogens or methyltetrahydrofolate in acetogens. MtaA can also utilize methylcobalamin as the methyl donor. Exemplary genes encoding MtaA can be found in methanogenic archaea such as Methanosarcina barkeri (Maeder et al., J. Bacteriol. 188:7922-7931(2006) and Methanosarcina acetivorans (Galagan et al., Genome Res. 12:532-542 (2002), as well as the acetogen, Moorella thermoacetica ((Das et al., Proteins 67:167-176 (2007)). In general, MtaA proteins that catalyze the transfer of the methyl group from CH₃-MtaC are difficult to identify bioinformatically as they share similarity to other corrinoid protein methyltransferases and are not oriented adjacent to the MtaB and MtaC genes on the chromosomes. Nevertheless, a number of MtaA encoding genes have been characterized. The protein sequences of these genes in M. barkeri and M. acetivorans can be identified by the following GenBank accession numbers.

Protein GenBank ID GI number Organism MtaA YP_304602 73668587 Methanosarcina barkeri MtaA1 NP_619241 20093166 Methanosarcina acetivorans MtaA2 NP_616548 20090473 Methanosarcina acetivorans

The MtaA gene, YP_304602, from M. barkeri was cloned, sequenced, and functionally overexpressed in E. coli (Harms and Thauer, Eur. J Biochem. 235:653-659 (1996)). In M. acetivorans, MtaA1 is required for growth on methanol, whereas MtaA2 is dispensable even though methane production from methanol is reduced in MtaA2 mutants (Bose et al., J. Bacteriol. 190:4017-4026 (2008)). There are multiple additional MtaA homologs in M. barkeri and M. acetivorans that areas yet uncharacterized, but may also catalyze corrinoid protein methyltransferase activity.

Putative MtaA encoding genes in M. thermoacetica were identified by their sequence similarity to the characterized methanogenic MtaA genes. Specifically, three M. thermoacetica genes show high homology (>30% sequence identity) to YP_304602 from M. barkeri. Unlike methanogenic MtaA proteins that naturally catalyze the transfer of the methyl group from CH₃-MtaC to Coenzyme M, an M. thermoacetica MtaA is likely to transfer the methyl group to methyltetrahydrofolate given the similar roles of methyltetrahydrofolate and Coenzyme M in methanogens and acetogens, respectively. The protein sequences of putative MtaA encoding genes from M. thermoacetica can be identified by the following GenBank accession numbers.

Protein GenBank ID GI number Organism MtaA YP_430937 83590928 Moorella thermoacetica MtaA YP_431175 83591166 Moorella thermoacetica MtaA YP_430935 83590926 Moorella thermoacetica MtaA YP_430064 83590056 Moorella thermoacetica

FIG. 4, Step B—Methylenetetrahydrofolate Reductase

The conversion of methyl-THF to methylenetetrahydrofolate is catalyzed by methylenetetrahydrofolate reductase. M. thermoacetica, this enzyme is oxygen-sensitive and contains an iron-sulfur cluster (Clark and Ljungdahl, J Biol. Chem. 259:10845-10849(1984). This enzyme is encoded by metF in E. coli (Sheppard et al., J. Bacteriol. 181:718-725 (1999) and CHY_1233 in C. hydrogenoformans(Wu et al., PLoS Genet. 1e65(2005). The M. thermoacetica genes, and its C. hydrogenoformans counterpart, are located near the CODH/ACS gene cluster, separated by putative hydrogenase and heterodisulfide reductase genes. Some additional gene candidates found bioinformatically are listed below. In Acetobacterium woodii metF is coupled to the Rnf complex through RnC2 (Poelein et al, PLoS One. 7:e33439). Homologs of RnC a found in other organisms by blast search. The Rnf complex is known to be reversible complex (Fuchs(2011) Annu. Rev. Microbiol. 65:631-658).

Protein GenBank ID GI number Organism Moth_1191 YP_430048.1 83590039 Moorella thermoacetica Moth_1192 YP_430049.1 83590040 Moorella thermoacetica metF NP_418376.1 16131779 Escherichia coli CHY_1233 YP_360071.1 78044792 Carboxydothermus hydrogenoformans CLJU_c37610 YP_003781889.1 300856905 Clostridium ljungdahlii DSM 13528 DesfrDRAFT_3717 ZP_07335241.1 303248996 Desulfovibrio fructosovorans JJ CcarbDRAFT_2950 ZP_05392950.1 255526026 Clostridium carboxidivorans P7 Ccel74_010100023124 ZP_07633513.1 307691067 Clostridium cellulovorans 743B Cphy_3110 YP_001560205.1 160881237 Clostridium phytofermentans ISDg

FIG. 4, Steps C and D—Methylenetetrahydrofolate Dehydrogenase, Methenyltetrahydrofolate Cyclohydrolase

In M. thermoacetica, E. coli, and C. hydrogenoformans, methenyltetrahydrofolate cyclohydrolase and methylenetetrahydrofolate dehydrogenase are carried out by the bi-functional gene products of Moth_1516, folD, and CHY_1878, respectively (Pierce et al., Environ. Microbiol. 10:2550-2573 (2008); Wu et al., PLoS Genet. 1:e65 (2005); D'Ari and Rabinowitz, J. Biol. Chem. 266:23953-23958 (1991)). A homolog exists in C. carboxidivorans P7. Several other organisms also encode for this bifunctional protein as tabulated below.

Protein GenBank ID GI number Organism Moth_1516 YP_430368.1 83590359 Moorella thermoacetica folD NP_415062.1 16128513 Escherichia coli CHY_1878 YP_360698.1 78044829 Carboxydothermus hydrogenoformans CcarbDRAFT_2948 ZP_05392948.1 255526024 Clostridium carboxidivorans P7 folD ADK16789.1 300437022 Clostridium ljungdahlii DSM 13528 folD-2 NP_951919.1 39995968 Geobacter sulfurreducens PCA folD YP_725874.1 113867385 Ralstonia eutropha H16 folD NP_348702.1 15895353 Clostridium acetobutylicum ATCC 824 folD YP_696506.1 110800457 Clostridium perfringens MGA3_09460 EIJ83438.1 387591119 Bacillus methanolicus MGA3 PB1_14689 ZP_10132349.1 387929672 Bacillus methanolicus PB1

FIG. 4, Step E—Formyltetrahydrofolate Deformylase

This enzyme catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-THF) to THF and formate. In E. coli, this enzyme is encoded by purU and has been overproduced, purified, and characterized (Nagy, et al., J. Bacteriol. 3:1292-1298 (1995)). Homologs exist in Corynebacterium sp. U-96 (Suzuki, et al., Biosci. Biotechnol. Biochem. 69(5):952-956 (2005)), Corynebacterium glutamicum ATCC 14067, Salmonella enterica, and several additional organisms.

Protein GenBank ID GI number Organism purU AAC74314.1 1787483 Escherichia coli K-12 MG1655 purU BAD97821.1 63002616 Corynebacterium sp. U-96 purU EHE84645.1 354511740 Corynebacterium glutamicum ATCC 14067 purU NP_460715.1 16765100 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

FIG. 4, Step F—Formyltetrahydrofolate Synthetase

Formyltetrahydrofolate synthetase ligates formate to tetrahydrofolate at the expense of one ATP. This reaction is catalyzed by the gene product of Moth_0109 in M. thermoacetica (O'brien et al., Experientia Suppl. 26:249-262 (1976); Lovell et al., Arch. Microbiol. 149:280-285 (1988); Lovell et al., Biochemistry 29:5687-5694 (1990)), FHS in Clostridium acidurici (Whitehead and Rabinowitz, J. Bacteriol. 167:203-209 (1986); Whitehead and Rabinowitz, J. Bacteriol. 170:3255-3261 (1988), and CHY_2385 in C. hydrogenoformans (Wu et al., PLoS Genet. 1:e65 (2005). Homologs exist in C. carboxidivorans P7. This enzyme is found in several other organisms as listed below.

Protein GenBank ID GI number Organism Moth_0109 YP_428991.1 83588982 Moorella thermoacetica CHY_2385 YP_361182.1 78045024 Carboxydothermus hydrogenoformans FHS P13419.1 120562 Clostridium acidurici CcarbDRAFT_1913 ZP_05391913.1 255524966 Clostridium carboxidivorans P7 CcarbDRAFT_2946 ZP_05392946.1 255526022 Clostridium carboxidivorans P7 Dhaf_0555 ACL18622.1 219536883 Desulfitobacterium hafniense fhs YP_001393842.1 153953077 Clostridium kluyveri DSM 555 fhs YP_003781893.1 300856909 Clostridium ljungdahlii DSM 13528 MGA3_08300 EIJ83208.1 387590889 Bacillus methanolicus MGA3 PB1_13509 ZP_10132113.1 387929436 Bacillus methanolicus PB1

FIG. 4, Step G—Formate Hydrogen Lyase

A formate hydrogen lyase enzyme can be employed to convert formate to carbon dioxide and hydrogen. An exemplary formate hydrogen lyase enzyme can be found in Escherichia coli. The E. coli formate hydrogen lyase consists of hydrogenase 3 and formate dehydrogenase-H (Maeda et al., Appl Microbiol Biotechnol 77:879-890 (2007)). It is activated by the gene product of fhlA. (Maeda et al., Appl Microbiol Biotechnol 77:879-890 (2007)). The addition of the trace elements, selenium, nickel and molybdenum, to a fermentation broth has been shown to enhance formate hydrogen lyase activity (Soini et al., Microb. Cell Fact. 7:26 (2008)). Various hydrogenase 3, formate dehydrogenase and transcriptional activator genes are shown below.

Protein GenBank ID GI number Organism hycA NP_417205 16130632 Escherichia coli K-12MG1655 hycB NP_417204 16130631 Escherichia coli K-12MG1655 hycC NP_417203 16130630 Escherichia coli K-12MG1655 hycD NP_417202 16130629 Escherichia coli K-12MG1655 hycE NP_417201 16130628 Escherichia coli K-12MG1655 hycF NP_417200 16130627 Escherichia coli K-12MG1655 hycG NP_417199 16130626 Escherichia coli K-12MG1655 hycH NP_417198 16130625 Escherichia coli K-12MG1655 hycI NP_417197 16130624 Escherichia coli K-12MG1655 fdhF NP_418503 16131905 Escherichia coli K-12MG1655 fhlA NP_417211 16130638 Escherichia coli K-12MG1655

A formate hydrogen lyase enzyme also exists in the hyperthermophilic archaeon, Thermococcus litoralis (Takacs et al., BMC. Microbiol 8:88 (2008)).

Protein GenBank ID GI number Organism mhyC ABW05543 157954626 Thermococcus litoralis mhyD ABW05544 157954627 Thermococcus litoralis mhyE ABW05545 157954628 Thermococcus litoralis myhF ABW05546 157954629 Thermococcus litoralis myhG ABW05547 157954630 Thermococcus litoralis myhH ABW05548 157954631 Thermococcus litoralis fdhA AAB94932 2746736 Thermococcus litoralis fdhB AAB94931 157954625 Thermococcus litoralis

Additional formate hydrogen lyase systems have been found in Salmonella typhimurium, Kebsiella pneumoniae, Rhodospirillum rubrum, Methanobactenium formicicum (Vardar-Schara et al., Microbial Biotechnology 1:107-125 (2008)).

FIG. 4. Step H—Hydrogenase

Hydrogenase enzymes can convert hydrogen gas to protons and transfer electrons to acceptors such as ferredoxins, NAD+, or NADP+. Ralstonia eutropha H16 uses hydrogen as an energy source with oxygen as a terminal electron acceptor. Its membrane-bound uptake [NiFe]-hydrogenase is an “O2-tolerant” hydrogenase (Cracknell, et al. Proc Nat Acad Sci, 106(49) 20681-20686 (2009)) that is periplasmically-oriented and connected to the respiratory chain via a b-type cytochrome (Schink and Schlegel, Biochim. Biophys. Acta, 567, 315-324 (1979); Bernhard et al., Eur. J Biochem. 248, 179-186 (1997)). R. eutropha also contains an O₂-tolerant soluble hydrogenase encoded by the Hox operon which is cytoplasmic and directly reduces NAD+ at the expense of hydrogen (Schneider and Schlegel, Biochim. Biophys. Acta 452, 66-80 (1976); Burgdorf J. Bact. 187(9) 3122-3132(2005)). Soluble hydrogenase enzymes are additionally present in several other organisms including Geobacter sulfurreducens (Coppi, Microbiology 151, 1239-1254 (2005)), Synechocystis str. PCC 6803 (Geimer, J. Biol. Chem., 284(52), 36462-36472 (2009)), and Thiocapsa roseopersicina (Rakhely, Appl. Environ. Microbiol. 70(2) 722-728 (2004)). The Synechocystis enzyme is capable of generating NADPH from hydrogen. Overexpression of both the Hox operon from Synechocystis str. PCC 6803 and the accessory genes encoded by the Hyp operon from Nostoc sp. PCC 7120 led to increased hydrogenase activity compared to expression of the Hox genes alone (Germer, J. Biol. Chem. 2452), 36462-36472 (2009))

Protein GenBank ID GI Number Organism HoxF NP_942727.1 38637753 Ralstonia eutropha H16 HoxU NP_942728.1 38637754 Ralstonia eutropha H16 HoxY NP_942729.1 38637755 Ralstonia eutropha H16 HoxH NP_942730.1 38637756 Ralstonia eutropha H16 HoxW NP_942731.1 38637757 Ralstonia eutropha H16 HoxI NP_942732.1 38637758 Ralstonia eutropha H16 HoxE NP_953767.1 39997816 Geobacter sulfurreducens HoxF NP_953766.1 39997815 Geobacter sulfurreducens HoxU NP_953765.1 39997814 Geobacter sulfurreducens HoxY NP_953764.1 39997813 Geobacter sulfurreducens HoxH NP_953763.1 39997812 Geobacter sulfurreducens GSU2717 NP_953762.1 39997811 Geobacter sulfurreducens HoxE NP_441418.1 16330690 Synechocystis str. PCC 6803 HoxF NP_441417.1 16330689 Synechocystis str. PCC 6803 Unknown function NP_441416.1 16330688 Synechocystis str. PCC 6803 HoxU NP_441415.1 16330687 Synechocystis str. PCC 6803 HoxY NP_441414.1 16330686 Synechocystis str. PCC 6803 Unknown function NP_441413.1 16330685 Synechocystis str. PCC 6803 Unknown function NP_441412.1 16330684 Synechocystis str. PCC 6803 HoxH NP_441411.1 16330683 Synechocystis str. PCC 6803 HypF NP_484737.1 17228189 Nostoc sp. PCC 7120 HypC NP_484738.1 17228190 Nostoc sp. PCC 7120 HypD NP_484739.1 17228191 Nostoc sp. PCC 7120 Unknown function NP_484740.1 17228192 Nostoc sp. PCC 7120 HypE NP_484741.1 17228193 Nostoc sp. PCC 7120 HypA NP_484742.1 17228194 Nostoc sp. PCC 7120 HypB NP_484743.1 17228195 Nostoc sp. PCC 7120 Hox1E AAP50519.1 37787351 Thiocapsa roseopersicina Hox1F AAP50520.1 37787352 Thiocapsa roseopersicina Hox1U AAP50521.1 37787353 Thiocapsa roseopersicina Hox1Y AAP50522.1 37787354 Thiocapsa roseopersicina Hox1H AAP50523.1 37787355 Thiocapsa roseopersicina

The genomes of E. coli and other enteric bacteria encode up to four hydrogenase enzymes (Sawers, G., Antonie Van Leeuwenhoek 66:57-88 (1994); Sawers et al., J. Bacteriol. 164:1324-1331(1985); Sawers and Boxer, Eur. J Biochem. 156:265-275 (1986); Sawers et al., J. Bacteriol. 168:398-404 (1986)). Given the multiplicity of enzyme activities E. coli another host organism can provide sufficient hydrogenase activity to split incoming molecular hydrogen and reduce the corresponding acceptor. Endogenous hydrogen-lyase enzymes of E. coli include hydrogenase 3, a membrane-bound enzyme complex using ferredoxin as an acceptor, and hydrogenase 4 that also uses a ferredoxin acceptor. Hydrogenase 3 and 4 are encoded by the hyc and hyf gene clusters, respectively. Hydrogenase activity in E. coli is also dependent upon the expression of the hyp genes whose corresponding proteins are involved in the assembly of the hydrogenase complexes (Jacobi et al., Arch. Microbiol 158:444-451(1992); Rangarajan et al., J. Bacteriol. 190:1447-1458 (2008)). The endogenous hydrogenase genes can be modified to increase the expression. For example, an endogenous gene having a naturally occurring inducible promoter can be up-regulated by providing the appropriate inducing agent, or the regulatory region of an endogenous gene can be engineered to incorporate an inducible regulatory element, thereby allowing the regulation of increased expression of an endogenous gene at a desired time. The M. thermoacetica and Clostridium ljungdahli hydrogenases are suitable for a host that lacks sufficient endogenous hydrogenase activity. M. thermoacetica and C. ljungdahli can grow with CO₂ as the exclusive carbon source indicating that reducing equivalents are extracted from H₂ to enable acetyl-CoA synthesis via the Wood-Ljungdahl pathway (Drake, H. L., J. Bacteriol. 150:702-709 (1982); Drake and Daniel, Res Microbiol 155:869-883 (2004); Kellum and Drake, J. Bacteriol. 160:466-469 (1984)). M. thermoacetica has homologs to several hyp, hyc, and hyf genes from E. coli. These protein sequences encoded for by these genes are identified by the following GenBank accession numbers. In addition, several gene clusters encoding hydrogenase functionality are present in M. thermoacetica and C. ljungdahli (see for example US2012/0003652).

Protein GenBank ID GI Number Organism HypA NP_417206 16130633 Escherichia coli HypB NP_417207 16130634 Escherichia coli HypC NP_417208 16130635 Escherichia coli HypD NP_417209 16130636 Escherichia coli HypE NP_417210 226524740 Escherichia coli HypF NP_417192 16130619 Escherichia coli HycA NP_417205 16130632 Escherichia coli HycB NP_417204 16130631 Escherichia coli HycC NP_417203 16130630 Escherichia coli HycD NP_417202 16130629 Escherichia coli HycE NP_417201 16130628 Escherichia coli HycF NP_417200 16130627 Escherichia coli HycG NP_417199 16130626 Escherichia coli HycH NP_417198 16130625 Escherichia coli HycI NP_417197 16130624 Escherichia coli HyfA NP_416976 90111444 Escherichia coli HyfB NP_416977 16130407 Escherichia coli HyfC NP_416978 90111445 Escherichia coli HyfD NP_416979 16130409 Escherichia coli HyfE NP_416980 16130410 Escherichia coli HyfF NP_416981 16130411 Escherichia coli HyfG NP_416982 16130412 Escherichia coli HyfH NP_416983 16130413 Escherichia coli HyfI NP_416984 16130414 Escherichia coli HyfJ NP_416985 90111446 Escherichia coli HyfR NP_416986 90111447 Escherichia coli

Proteins in M. thermoacetica whose genes are homologous to the E. coli hydrogenase genes are shown below.

Protein GenBank ID GI Number Organism Moth_2175 YP_431007 83590998 Moorella thermoacetica Moth_2176 YP_431008 83590999 Moorella thermoacetica Moth_2177 YP_431009 83591000 Moorella thermoacetica Moth_2178 YP_431010 83591001 Moorella thermoacetica Moth_2179 YP_431011 83591002 Moorella thermoacetica Moth_2180 YP_431012 83591003 Moorella thermoacetica Moth_2181 YP_431013 83591004 Moorella thermoacetica Moth_2182 YP_431014 83591005 Moorella thermoacetica Moth_2183 YP_431015 83591006 Moorella thermoacetica Moth_2184 YP_431016 83591007 Moorella thermoacetica Moth_2185 YP_431017 83591008 Moorella thermoacetica Moth_2186 YP_431018 83591009 Moorella thermoacetica Moth_2187 YP_431019 83591010 Moorella thermoacetica Moth_2188 YP_431020 83591011 Moorella thermoacetica Moth_2189 YP_431021 83591012 Moorella thermoacetica Moth_2190 YP_431022 83591013 Moorella thermoacetica Moth_2191 YP_431023 83591014 Moorella thermoacetica Moth_2192 YP_431024 83591015 Moorella thermoacetica Moth_0439 YP_429313 83589304 Moorella thermoacetica Moth_0440 YP_429314 83589305 Moorella thermoacetica Moth_0441 YP_429315 83589306 Moorella thermoacetica Moth_0442 YP_429316 83589307 Moorella thermoacetica Moth_0809 YP_429670 83589661 Moorella thermoacetica Moth_0810 YP_429671 83589662 Moorella thermoacetica Moth_0811 YP_429672 83589663 Moorella thermoacetica Moth_0812 YP_429673 83589664 Moorella thermoacetica Moth_0814 YP_429674 83589665 Moorella thermoacetica Moth_0815 YP_429675 83589666 Moorella thermoacetica Moth_0816 YP_429676 83589667 Moorella thermoacetica Moth_1193 YP_430050 83590041 Moorella thermoacetica Moth_1194 YP_430051 83590042 Moorella thermoacetica Moth_1195 YP_430052 83590043 Moorella thermoacetica Moth_1196 YP_430053 83590044 Moorella thermoacetica Moth_1717 YP_430562 83590553 Moorella thermoacetica Moth_1718 YP_430563 83590554 Moorella thermoacetica Moth_1719 YP_430564 83590555 Moorella thermoacetica Moth_1883 YP_430726 83590717 Moorella thermoacetica Moth_1884 YP_430727 83590718 Moorella thermoacetica Moth_1885 YP_430728 83590719 Moorella thermoacetica Moth_1886 YP_430729 83590720 Moorella thermoacetica Moth_1887 YP_430730 83590721 Moorella thermoacetica Moth_1888 YP_430731 83590722 Moorella thermoacetica Moth_1452 YP_430305 83590296 Moorella thermoacetica Moth_1453 YP_430306 83590297 Moorella thermoacetica Moth_1454 YP_430307 83590298 Moorella thermoacetica

Genes encoding hydrogenase enzymes from C. ljungdahli are shown below.

Protein GenBank ID GI Number Organism CLJU_c20290 ADK15091.1 300435324 Clostridium ljungdahli CLJU_c07030 ADK13773.1 300434006 Clostridium ljungdahli CLJU_c07040 ADK13774.1 300434007 Clostridium ljungdahli CLJU_c07050 ADK13775.1 300434008 Clostridium ljungdahli CLJU_c07060 ADK13776.1 300434009 Clostridium ljungdahli CLJU_c07070 ADK13777.1 300434010 Clostridium ljungdahli CLJU_c07080 ADK13778.1 300434011 Clostridium ljungdahli CLJU_c14730 ADK14541.1 300434774 Clostridium ljungdahli CLJU_c14720 ADK14540.1 300434773 Clostridium ljungdahli CLJU_c14710 ADK14539.1 300434772 Clostridium ljungdahli CLJU_c14700 ADK14538.1 300434771 Clostridium ljungdahli CLJU_c28670 ADK15915.1 300436148 Clostridium ljungdahli CLJU_c28660 ADK15914.1 300436147 Clostridium ljungdahli CLJU_c28650 ADK15913.1 300436146 Clostridium ljungdahli CLJU_c28640 ADK15912.1 300436145 Clostridium ljungdahli

In some cases, hydrogenase encoding genes are located adjacent to a CODH. In Rhodospirillum rubrum, the encoded CODH/hydrogenase proteins form a membrane-bound enzyme complex that has been indicated to be a site where energy, in the form of a proton gradient, is generated from the conversion of CO and H₂O to CO₂ and H₂ (Fox et al., J Bacteriol. 178:6200-6208 (1996)). The CODH-I of C. hydrogenoformans and its adjacent genes have been proposed to catalyze a similar functional role based on their similarity to the R. rubrum CODH/hydrogenase gene cluster (Wu et al., PLoS Genet. 1:e65 (2005)). The C. hydrogenoformans CODH-I was also shown to exhibit intense CO oxidation and CO₂ reduction activities when linked to an electrode (Parkin et al., J Am. Chem. Soc. 129:10328-10329 (2007)).

Protein GenBank ID GI Number Organism CooL AAC45118 1515468 Rhodospirillum rubrum CooX AAC45119 1515469 Rhodospirillum rubrum CooU AAC45120 1515470 Rhodospirillum rubrum CooH AAC45121 1498746 Rhodospirillum rubrum CooF AAC45122 1498747 Rhodospirillum rubrum CODH (CooS) AAC45123 1498748 Rhodospirillum rubrum CooC AAC45124 1498749 Rhodospirillum rubrum CooT AAC45125 1498750 Rhodospirillum rubrum Cool AAC45126 1498751 Rhodospirillum rubrum CODH-I (CooS-I) YP_360644 78043418 Carboxydothermus hydrogenoformans CooF YP_360645 78044791 Carboxydothermus hydrogenoformans HypA YP_360646 78044340 Carboxydothermus hydrogenoformans CooH YP_360647 78043871 Carboxydothermus hydrogenoformans CooU YP_360648 78044023 Carboxydothermus hydrogenoformans CooX YP_360649 78043124 Carboxydothermus hydrogenoformans CooL YP_360650 78043938 Carboxydothermus hydrogenoformans CooK YP_360651 78044700 Carboxydothermus hydrogenoformans CooM YP_360652 78043942 Carboxydothermus hydrogenoformans CooC YP_360654.1 78043296 Carboxydothermus hydrogenoformans CooA-1 YP_360655.1 78044021 Carboxydothermus_hydrogenoformans

Some hydrogenase and CODH enzymes transfer electrons to ferredoxins. Ferredoxins are small acidic proteins containing one or more iron-sulfur clusters that function as intracellular electron carriers with a low reduction potential. Reduced ferredoxins donate electrons to Fe-dependent enzymes such as ferredoxin-NADP⁺ oxidoreductase, pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OFOR). The H. thermophilus gene fdx1 encodes a[41Fe4S]-type ferredoxin that is required for the reversible carboxylation of 2-oxoglutarate and pyruvate by OFOR and PFOR, respectively (Yamamoto et al., Extremophiles 14:79-85 (2010)). The ferredoxin associated with the Sulfolobus solfataricus 2-oxoacid:ferredoxin reductase is a monomeric dicluster [3Fe-4S4Fe-4S] type ferredoxin (Park et al. J Biochem Mol Biol. 2006 Jan. 31; 39(1):46-54.). The N-terminal domain of the protein shares 93% homology with the zfx ferredoxin from S. acidocaldarius. The E. coli genome encodes a soluble ferredoxin of unknown physiological function, fdx. Some evidence indicates that this protein can function in iron-sulfur cluster assembly (Takahashi and Nakamura, J Biochem. 1999 November; 126(5):917-26). Additional ferredoxin proteins have been characterized in Helicobacter pylori (Mukhopadhyay et al. J. Bacteriol. 2003 May; 185(9):2927-35) and Campylobacter jejuni (van Vliet et al. FEMS Microbiol Lett. 2001 Mar. 15; 196(2):189-93). A2Fe-2S ferredoxin from Clostridium pasteurianum has been cloned and expressed in E. coli(Fujinaga and Meyer, Biochemical and Biophysical Research Communications, 192(3): (1993)). Acetogenic bacteria such as Moorella thermoacetica, Clostridium carboxidivorans P7, Clostridium ljungdahli and Rhodospirillum rubrum are predicted to encode several ferredoxins, listed below.

Protein GenBank ID GI Number Organism fdx1 BAE02673.1 68163284 Hydrogenobacter thermophilus M11214.1 AAA83524.1 144806 Clostridium pasteurianum Zfx AAY79867.1 68566938 Sulfolobus acidocalarius Fdx AAC75578.1 1788874 Escherichia coli hp 0277 AAD07340.1 2313367 Helicobacter pylori fdxA CAL34484.1 112359698 Campylobacter jejuni Moth 0061 ABC18400.1 83571848 Moorella thermoacetica Moth 1200 ABC19514.1 83572962 Moorella thermoacetica Moth 1888 ABC20188.1 83573636 Moorella thermoacetica Moth_2112 ABC20404.1 83573852 Moorella thermoacetica Moth_1037 ABC19351.1 83572799 Moorella thermoacetica CcarbDRAFT_4383 ZP_05394383.1 255527515 Clostridium carboxidivorans P7 CcarbDRAFT_2958 ZP_05392958.1 255526034 Clostridium carboxidivorans P7 CcarbDRAFT_2281 ZP_05392281.1 255525342 Clostridium carboxidivorans P7 CcarbDRAFT_5296 ZP_05395295.1 255528511 Clostridium carboxidivorans P7 CcarbDRAFT_1615 ZP_05391615.1 255524662 Clostridium carboxidivorans P7 CcarbDRAFT_1304 ZP_05391304.1 255524347 Clostridium carboxidivorans P7 cooF AAG29808.1 11095245 Carboxydothermus hydrogenoformans fdxN CAA35699.1 46143 Rhodobacter capsulatus Rru_A2264 ABC23064.1 83576513 Rhodospirillum rubrum Rru_A1916 ABC22716.1 83576165 Rhodospirillum rubrum Rru_A2026 ABC22826.1 83576275 Rhodospirillum rubrum cooF AAC45122.1 1498747 Rhodospirillum rubrum fdxN AAA26460.1 152605 Rhodospirillum rubrum Alvin_2884 ADC63789.1 288897953 Allochromatium vinosum DSM 180 Fdx YP_002801146.1 226946073 Azotobacter vinelandii DJ CKL_3790 YP_001397146.1 153956381 Clostridium kluyveri DSM 555 fer1 NP_949965.1 39937689 Rhodopseudomonas palustris CGA009 Fdx CAA12251.1 3724172 Thauera aromatica CHY_2405 YP_361202.1 78044690 Carboxydothermus hydrogenoformans Fer YP_359966.1 78045103 Carboxydothermus hydrogenoformans Fer AAC83945.1 1146198 Bacillus subtilis fdx1 NP_249053.1 15595559 Pseudomonas aeruginosa PA01 yfhL AP_003148.1 89109368 Escherichia coli K-12 CLJU_c00930 ADK13195.1 300433428 Clostridium ljungdahli CLJU_c00010 ADK13115.1 300433348 Clostridium ljungdahli CLJU_c01820 ADK13272.1 300433505 Clostridium ljungdahli CLJU c17980 ADK14861.1 300435094 Clostridium ljungdahli CLJU c17970 ADK14860.1 300435093 Clostridium ljungdahli CLJU c22510 ADK15311.1 300435544 Clostridium ljungdahli CLJU_c26680 ADK15726.1 300435959 Clostridium ljungdahli CLJU_c29400 ADK15988.1 300436221 Clostridium ljungdahli

Ferredoxin oxidoreductase enzymes transfer electrons firm ferredoxins or flavodoxins to NAD(P)H. Two enzymes catalyzing the reversible transfer of electrons firm reduced ferredoxins to NAD(P)+ are ferredoxin:NAD+ oxidoreductase (EC 1.18.13) and ferredoxin:NADP+ oxidoreductase (FNR, EC 1.18.1.2). Ferredoxin:NADP+ oxidoreductase (FNR, EC 1.18.1.2) has a noncovalently bound FAD cofactor that facilitates the reversible transfer of electrons from NADPH to low-potential acceptors such as ferredoxins or flavodoxins (Blaschkowsici et al., Eur. J. Biochem. 123:563-569 (1982); Fuji et al., Biochemistry. 1997 Feb. 11; 36(6):1505-13). The Helicobacter pylori FNR, encoded by HP1164 (fgrB), is coupled to the activity of pyruvate:ferredoxin oxidoreductase (PFOR) resulting in the pyruvac-dependent production of NADPH (St Maurice et al., J. Bacteriol. 189:4764-4773 (2007)). An analogous enzyme is found in Campylobacter jejuni (St Maurice et al., J. Bacteriol 189:4764-4773 (2007)). A ferredoxin:NADP+ oxidoreductase enzyme is encoded in the E. coli genome by fpr (Bianchi et al. J. Bacteriol. 1993 March, 175(6):1590-5). Ferredoxin:NAD+ oxidoreductase utilizes reduced ferredoxin to generate NADH firm NAD+. In several organisms, including E. coli, this enzyme is a component of multifunctional dioxygenase enzyme complexes. The ferredoxin:NAD+ oxidoreductase of E. coli, encoded by haaD, is a component of the 3-phenylproppionate dioxygenase system involved in involved in aromatic acid utilization (Diaz et al. J. Bacteriol. 1998 June; 180(11):2915-23). NADH:ferredoxin reductase activity was detected in cell extracts of Hydrogenobacter thermophilus, although a gene with this activity has not yet been indicated (Yoon et al. Arch Microbiol. 1997 May; 167(5):275-9). Additional ferredoxin:NAD(P)+ oxidoreductases have been annotated in Clostridium carboxydivorans P7. The NADH-dependent reduced ferredoxin: NADP oxidoreductase of C. kluyveri, encoded by nfnAB, catalyzes the concomitant reduction of ferredoxin and NAD+ with two equivalents of NADPH (Wang et al, J Bacteriol 192: 5115-5123 (2010)). Finally, the energy-conserving membrane-associated Riff-type proteins (Seedorf et al, PNAS 105:2128-2133 (2008); and Hermann, J. Bacteriol 190:784-791(2008)) provide a means to generate NADH or NADPH from reduced ferredoxin.

Protein GenBank ID GI Number Organism fqrB NP_207955.1 15645778 Helicobacter pylori fqrB YP_001482096.1 157414840 Campylobacter jejuni RPA3954 CAE29395.1 39650872 Rhodopseudomonas palustris Fpr BAH29712.1 225320633 Hydrogenobacter thermophilus yumC NP_391091.2 255767736 Bacillus subtilis Fpr P28861.4 399486 Escherichia coli hcaD AAC75595.1 1788892 Escherichia coli LOC100282643 NP_001149023.1 226497434 Zea mays NfnA YP_001393861.1 153953096 Clostridium kluyveri NfnB YP_001393862.1 153953097 Clostridium kluyveri CcarbDRAFT_2639 ZP_05392639.1 255525707 Clostridium carboxidivorans P7 CcarbDRAFT_2638 ZP_05392638.1 255525706 Clostridium carboxidivorans P7 CcarbDRAFT 2636 ZP_05392636.1 255525704 Clostridium carboxidivorans P7 CcarbDRAFT 5060 ZP_05395060.1 255528241 Clostridium carboxidivorans P7 CcarbDRAFT_2450 ZP_05392450.1 255525514 Clostridium carboxidivorans P7 CcarbDRAFT_1084 ZP_05391084.1 255524124 Clostridium carboxidivorans P7 RnfC EDK33306.1 146346770 Clostridium kluyveri RnfD EDK33307.1 146346771 Clostridium kluyveri RnfG EDK33308.1 146346772 Clostridium kluyveri RnfE EDK33309.1 146346773 Clostridium kluyveri RnfA EDK33310.1 146346774 Clostridium kluyveri RnfB EDK33311.1 146346775 Clostridium kluyveri CLJU c11410 (RnfB) ADK14209.1 300434442 Clostridium ljungdahlii CLJU_c11400 (RnfA) ADK14208.1 300434441 Clostridium ljungdahlii CLJU_c11390 (RnfE) ADK14207.1 300434440 Clostridium ljungdahlii CLJU_c11380 (RnfG) ADK14206.1 300434439 Clostridium ljungdahlii CLJU c11370 (RnfD) ADK14205.1 300434438 Clostridium ljungdahlii CLJU c11360 (RnfC) ADK14204.1 300434437 Clostridium ljungdahlii MOTH_1518 (NfnA) YP_430370.1 83590361 Moorella thermoacetica MOTH_1517(NfnB) YP_430369.1 83590360 Moorella thermoacetica CHY_1992 (NfnA) YP_360811.1 78045020 Carboxydothermus hydrogenoformans CHY 1993 (NfnB) YP_360812.1 78044266 Carboxydothermus hydrogenoformans CLJU c37220 (NfnAB) YP_003781850.1 300856866 Clostridium ljungdahlii

FIG. 4, Step I—Formate Dehydrogenase

Formate dehydrogenase (FDH) catalyzes the reversible transfer of electrons from formate to an acceptor. Enzymes with FDH activity utilize various electron Gathers such as, for example, NADH (EC 1.2.1.2), NADPH (EC 1.2.1.43), quinols (EC 1.1.5.6), cytochromes (EC 1.2.2.3) and hydrogenases (EC 1.1.99.33). FDH enzymes have been characterized from Moorella thermoacetica (Andreesen and Ljungdahl, J Bacteriol 116:867-873 (1973); Li et al., J Bacteriol 92:405-412 (1966); Yamamoto et al., J Biol Chem. 258:1826-1832 (1983). The loci, Moth_2312 is responsible for encoding the alpha subunit of formate dehydrogenase while the beta subunit is encoded by Moth_2314 (Pierce et al., Environ Microbiol (2008)). Another set of genes encoding formate dehydrogenase activity with a propensity for CO₂ reduction is encoded by Sfum_2703 through Sfum_2706 in Syntrophobacter fumaroxidans (de Bok et al., Eur J Biochem. 270:2476-2485 (2003)); Reda et al., PNAS 105:10654-10658 (2008)). A similar set of genes presumed to carry out the same function are encoded by CHY_0731, CHY_0732, and CHY_0733 in C. hydrogenoformans (Wu et al., PLoS Genet 1:e65 (2005)). Formate dehydrogenases are also found many additional organisms including C. carboxidivorans P7, Bacillus methanolicus, Burkholderia stabilis, Moorella thermoacetica ATCC 39073, Candida boidinii, Candida methylica, and Saccharomyces cerevisiae S288c. The soluble formate dehydrogenase from Ralstonia eutropha reduces NAD⁺ (fdsG, -B, -A, -C, -D) (Oh and Bowien., 1998)

Protein GenBank ID GI Number Organism Moth_2312 YP_431142 148283121 Moorella thermoacetica Moth 2314 YP_431144 83591135 Moorella thermoacetica Sfum_2703 YP_846816.1 116750129 Syntrophobacter fumaroxidans Sfum_2704 YP_846817.1 116750130 Syntrophobacter fumaroxidans Sfum_2705 YP_846818.1 116750131 Syntrophohacter fumaroxidans Sfum_2706 YP_846819.1 116750132 Syntrophobacter fumaroxidans CHY_0731 YP_359585.1 78044572 Carboxydothermus hydrogenoformans CHY_0732 YP_359586.1 78044500 Carboxydothermus hydrogenoformans CHY_0733 YP_359587.1 78044647 Carboxydothermus hydrogenoformans CcarbDRAFT_0901 ZP_05390901.1 255523938 Clostridium carboxidivorans P7 CcarbDRAFT_4380 ZP_05394380.1 255527512 Clostridium carboxidivorans P7 fdhA, MGA3_06625 EIJ82879.1 387590560 Bacillus methanolicus MGA3 fdhA, PB1_11719 ZP_10131761.1 387929084 Bacillus methanolicus PB1 fdhD, MGA3_06630 EIJ82880.1 387590561 Bacillus methanolicus MGA3 fdhD, PB1_11724 ZP_10131762.1 387929085 Bacillus methanolicus PB1 fdh ACF35003. 194220249 Burkholderia stabilis FDH1 AAC49766.1 2276465 Candida boidinii fdh CAA57036.1 1181204 Candida methylica FDH2 P0CF35.1 294956522 Saccharomyces cerevisiae S288c FDH1 NP_015033.1 6324964 Saccharomyces cerevisiae S288c fdsG YP_725156.1 113866667 Ralstonia eutropha fdsB YP_725157.1 113866668 Ralstonia eutropha fdsA YP_725158.1 113866669 Ralstonia eutropha fdsC YP_725159.1 113866670 Ralstonia eutropha fdsD YP_725160.1 113866671 Ralstonia eutropha

FIG. 4, Step J, FIG. 3, Step a—Methanol Dehydrogenase

NAD+ dependent methanol dehydrogenase enzymes (EC 1.1.1.244) catalyze the conversion of methanol and NAD+ to formaldehyde and NADH. An enzyme with this activity was first characterized in Bacillus methanolicus (Heggeset, et al., Applied and Environmental Microbiology, 78(15):5170-5181(2012)). This enzyme is zinc and magnesium dependent, and activity of the enzyme is enhanced by the activating enzyme encoded by act (Kloosterman et al, J Biol Chem 277:34785-92 (2002)). The act is a Nudix hydrolase. Several of these candidates have been identified and shown to have activity on methanol. Additional NAD(P)+ dependent enzymes can be identified by sequence homology. Methanol dehydrogenase enzymes utilizing different electron acceptors are also known in the art. Examples include cytochrome dependent enzymes such as mxaIF of the methylotroph Methylobacterium extorquens (Nunn et al, Nucl Acid Res 16:7722 (1988)). Methanol dehydrogenase enzymes of methanotrophs such as Methylococcus capsulatis function in a complex with methane monooxygenase (MMO) (Myronova et al, Biochem 45:11905-14 (2006)). Methanol can also be oxidized to formaldehyde by alcohol oxidase enzymes such as methanol oxidase (EC 1.1.3.13) of Candida boidinii (Sakai et al. Gene 114: 67-73 (1992)).

Protein GenBank ID GI Number Organism mdh, MGA3_17392 EIJ77596.1 387585261 Bacillus methanolicus MGA3 mdh2, MGA3_07340 EIJ83020.1 387590701 Bacillus methanolicus MGA3 mdh3, MGA3_10725 EIJ80770.1 387588449 Bacillus methanolicus MGA3 act, MGA3_09170 EIJ83380.1 387591061 Bacillus methanolicus MGA3 mdh, PB1_17533 ZP_10132907.1 387930234 Bacillus methanolicus PB1 mdh1, PB1_14569 ZP_10132325.1 387929648 Bacillus methanolicus PB1 mdh2, PB1_12584 ZP_10131932.1 387929255 Bacillus methanolicus PB1 act, PB1_14394 ZP_10132290.1 387929613 Bacillus methanolicus PB1 BFZC1_05383 ZP_07048751.1 299535429 Lysinibacillus fusiformis BFZC1_20163 ZP_07051637.1 299538354 Lysinibacillus fusiformis Bsph_4187 YP_001699778.1 169829620 Lysinibacillus sphaericus Bsph_1706 YP_001697432.1 169827274 Lysinibacillus sphaericus mdh2 YP_004681552.1 339322658 Cupriavidus necator N-1 nudF1 YP_004684845.1 339325152 Cupriavidus necator N-1 BthaA_010200007655 ZP_05587334.1 257139072 Burkholderia thailandensis E264 BTH_I1076 YP_441629.1 83721454 Burkholderia thailandensis E264 (MutT/NUDIX NTP pyrophosphatase) BalcAV_11743 ZP_10819291.1 402299711 Bacillus alcalophilus ATCC 27647 BalcAV_05251 ZP_10818002.1 402298299 Bacillus alcalophilus ATCC 27647 alcohol dehydrogenase YP_001447544 156976638 Vibrio harveyi ATCC BAA-1116 P3TCK_27679 ZP_01220157.1 90412151 Photobacterium profundum 3TCK alcohol dehydrogenase YP_694908 110799824 Clostridium perfringens ATCC 13124 adhB NP_717107 24373064 Shewanella oneidensis MR-1 alcohol dehydrogenase YP_237055 66047214 Pseudomonas syringae pv. syringae B728a alcohol dehydrogenase YP_359772 78043360 Carboxydothermus hydrogenoformans Z-2901 alcohol dehydrogenase YP_003990729 312112413 Geobacillus sp. Y4.1MC1 PpeoK3_010100018471 ZP_10241531.1 390456003 Paenibacillus peoriae KCTC 3763 OBE_12016 EKC54576 406526935 human gut metagenome alcohol dehydrogenase YP_001343716 152978087 Actinobacillus succinogenes 130Z dhaT AAC45651 2393887 Clostridium pasteurianum DSM 525 alcohol dehydrogenase NP_561852 18309918 Clostridium perfringens str. 13 BAZO_10081 ZP_11313277.1 410459529 Bacillus azotoformans LMG 9581 alcohol dehydrogenase YP_007491369 452211255 Methanosarcina mazei Tuc01 alcohol dehydrogenase YP_004860127 347752562 Bacillus coagulans 36D1 alcohol dehydrogenase YP_002138168 197117741 Geobacter bemidjiensis Bem DesmeDRAFT_1354 ZP_08977641.1 354558386 Desulfitobacterium metallireducens DSM 15288 alcohol dehydrogenase YP_001337153 152972007 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 alcohol dehydrogenase YP_001113612 134300116 Desulfotomaculum reducens MI-1 alcohol dehydrogenase YP_001663549 167040564 Thermoanaerobacter sp. X514 ACINNAV82_2382 ZP_16224338.1 421788018 Acinetobacter baumannii Naval-82 alcohol dehydrogenase YP_005052855 374301216 Desulfovibrio africanus str. Walvis Bay alcohol dehydrogenase AGF87161 451936849 uncultured organism DesfrDRAFT_3929 ZP_07335453.1 303249216 Desulfovibrio fructosovorans JJ alcohol dehydrogenase NP_617528 20091453 Methanosarcina acetivorans C2A alcohol dehydrogenase NP_343875.1 15899270 Sulfolobus solfataricus P-2 adh4 YP_006863258 408405275 Nitrososphaera gargensis Ga9.2 Ta0841 NP_394301.1 16081897 Thermoplasma acidophilum PTO1151 YP_023929.1 48478223 Picrophilus torridus DSM9790 alcohol dehydrogenase ZP_10129817.1 387927138 Bacillus methanolicus PB-1 cgR_2695 YP_001139613.1 145296792 Corynebacterium glutamicum R alcohol dehydrogenase YP_004758576.1 340793113 Corynebacterium variabile HMPREF1015_01790 ZP_09352758.1 365156443 Bacillus smithii ADH1 NP_014555.1 6324486 Saccharomyces cerevisiae NADH-dependent butanol YP_001126968.1 138896515 Geobacillus themodenitrificans NG80-2 dehydrogenase A alcohol dehydrogenase WP 007139094.1 494231392 Flavobacterium frigoris methanol dehydrogenase WP 003897664.1 489994607 Mycobacterium smegmatis ADH1B NP_000659.2 34577061 Homo sapiens PMI01_01199 ZP_10750164.1 399072070 Caulobacter sp. AP07 YiaY YP_026233.1 49176377 Escherichia coli MCA0299 YP_112833.1 53802410 Methylococcus capsulatis MCA0782 YP_113284.1 53804880 Methylococcus capsulatis mxaI YP_002965443.1 240140963 Methylobacterium extorquens mxaF YP_002965446.1 240140966 Methylobacterium extorquens AOD1 AAA34321.1 170820 Candida boidinii hypothetical protein EDA87976.1 142827286 Marine metagenome GOS_1920437 JCVI_SCAF_1096627185304 alcohol dehydrogenase CAA80989.1 580823 Geobacillus stearothermophilus

An in vivo assay was developed to determine the activity of methanol dehydrogenases. This assay relies on the detection of formaldehyde (HCHO), thus measuring the forward activity of the enzyme (oxidation of methanol). To this end, a strain comprising a BDOP and lacking frmA, frmB, frmR was created using Lambda Red recombinase technology (Datsenko and Wanner, Proc. Natl. Acad. Sci. USA, 6 97(12): 6640-5 (2000). Plasmids expressing methanol dehydrogenases were transformed into the strain, then grown to saturation in LB medium+ antibiotic at 37° C. with shaking. Transformation of the strain with an empty vector served as a negative control. Cultures were adjusted by O.D. and then diluted 1:10 into M9 medium+0.5% glucose+ antibiotic and cultured at 37° C. with shaking for 6-8 hours until late log phase. Methanol was added to 2% v/v and the cultures were further incubated for 30 min. with shaking at 37° C. Cultures were spun down and the supernatant was assayed for formaldehyde produced using DETECTX Formaldehyde Detection kit (Arbor Assays; Ann Arbor, Mich.) according to manufacturer's instructions. The frmA, frmB, frmR deletions resulted in the native formaldehyde utilization pathway to be deleted, which enables the formation of formaldehyde that can be used to detect methanol dehydrogenase activity in the non-naturally occurring microbial organism.

The activity of several enzymes was measured using the assay described above. The results of four independent experiments are provided in the Table below.

Results of in vivo assays showing formaldehyde (HCHO) production by various non-naturally occurring microbial organism comprising a plasmid expressing a methanol dehydrogenase.

Accession number HCHO (μM) Experiment 1 EIJ77596.1 >50 EIJ83020.1 >20 EIJ80770.1 >50 ZP_10132907.1 >20 ZP_10132325.1 >20 ZP_10131932.1 >50 ZP_07048751.1 >50 YP_001699778.1 >50 YP_004681552.1 >10 ZP_10819291.1 <1 Empty vector 2.33 Experiment 2 EIJ77596.1 >50 NP_00659.2 >50 YP_004758576.1 >20 ZP_09352758.1 >50 ZP_10129817.1 >20 YP_001139613.1 >20 NP_014555.1 >10 WP_007139094.1 >10 NP_343875.1 >1 YP_006863258 >1 NP_394301.1 >1 ZP_10750164.1 >1 YP_023929.1 >1 ZP_08977641.1 <1 ZP_10117398.1 <1 YP_004108045.1 <1 ZP_09753449.1 <1 Empty vector 0.17 Experiment 3 EIJ77596.1 >50 NP_561852 >50 YP_002138168 >50 YP_026233.1 >50 YP_001447544 >50 Metalibrary >50 YP_359772 >50 ZP_01220157.1 >50 ZP_07335453.1 >20 YP_001337153 >20 YP_694908 >20 NP_717107 >20 AAC45651 >10 ZP_11313277.1 >10 ZP_16224338.1 >10 YP_001113612 >10 YP_004860127 >10 YP_003310546 >10 YP_001343716 >10 NP_717107 >10 YP_002434746 >10 Empty vector 0.11 Experiment 4 EIJ77596.1 >20 ZP_11313277.1 >50 YP_001113612 >50 YP_001447544 >20 AGF87161 >50 EDA87976.1 >20 Empty vector −0.8

FIG. 4, Step K— Spontaneous or Formaldehyde Activating Enzyme

The conversion of formaldehyde and THF to methylenetetrahydrofolate can occur spontaneously. It is also possible that the rate of this reaction can be enhanced by a formaldehyde activating enzyme. A formaldehyde activating enzyme (Fae) has been identified in Methylobacterium extorquens AM1 which catalyzes the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin (Vorholt, et al., J. Bacteriol., 182(23), 6645-6650 (2000)). It is possible that a similar enzyme exists or can be engineered to catalyze the condensation of formaldehyde and tetrahydrofolate to methylenetetrahydrofolate. Homologs exist in several organisms including Xanthobacter autotrophicus Py2 and Hyphomicrobium denitrificans ATCC 51888.

Protein GenBank ID GI Number Organism MexAM1_META1p1766 Q9FA38.3 17366061 Methylobacterium extorquens AM1 Xaut_0032 YP_001414948.1 154243990 Xanthobacter autotrophicus Py2 Hden_1474 YP_003755607.1 300022996 Hyphomicrobium denitrificans ATCC 51888

FIG. 4, Step L—Formaldehyde Dehydrogenase

Oxidation of formaldehyde to formate is catalyzed by formaldehyde dehydrogenase. An NAD+ dependent formaldehyde dehydrogenase enzyme is encoded by fdhA of Pseudomonas putida (Ito et al, J. Bacteriol 176: 2483-2491(1994)). Additional formaldehyde dehydrogenase enzymes include the NAD+ and glutathione independent formaldehyde dehydrogenase from Hyphomicrobium zavarzinii (Jerome et al, Appl Microbiol Biotechnol 77:779-88 (2007)), the glutathione dependent formaldehyde dehydrogenase of Pichia pastoris (Sunga et al, Gene 330:3947 (2004)) and the NAD(P)+ dependent formaldehyde dehydrogenase of Methylobacter marinus (Speer et al, FEMS Microbiol Lett, 121(3):349-55 (1994)).

Protein GenBank ID GI Number Organism fdhA P46154.3 1169603 Pseudomonas putida faoA CAC85637.1 19912992 Hyphomicrobium zavarzinii Fld1 CCA39112.1 328352714 Pichia pastoris fdh P47734.2 221222447 Methylobacter marinus

In addition to the formaldehyde dehydrogenase enzymes listed above, alternate enzymes and pathways for converting formaldehyde to formate are known in the art. For example, many organisms employ glutathione-dependent formaldehyde oxidation pathways, in which formaldehyde is converted to formate in three steps via the intermediates S-hydroxymethylglutathione and S-formylglutathione (Vorholt et al, J. Bacteriol 182:6645-50 (2000)). The enzymes of this pathway are S-(hydroxymethyl)glutathione synthase (EC 4.4.1.22), glutathione-dependent formaldehyde dehydrogenase (EC 1.1.1.284) and S-formylglutathione hydrolase (EC 3.1.2.12).

FIG. 4, Step M—Spontaneous or S-(Hydroxymethyl)Glutathione Synthase

While conversion of formaldehyde to S-hydroxymethylglutathione can occur spontaneously in the presence of glutathione, it has been shown by Goenrich et al (Goenrich, et al., J Biol Chem 277(5); 3069-72 (2002)) that an enzyme from Paracoccus denitrificans can accelerate this spontaneous condensation reaction. The enzyme catalyzing the conversion of formaldehyde and glutathione was purified and named glutathione-dependent formaldehyde-activating enzyme (Gfa). The gene encoding it, which was named gfa, is located directly upstream of the gene for glutathione-dependent formaldehyde dehydrogenase, which catalyzes the subsequent oxidation of S-hydroxymethylglutathione. Putative proteins with sequence identity to Gfa from P. denitrificans are present also in Rhodobacter sphaeroides, Sinorhizobium meliloti, and Mesorhizobium loti.

Protein GenBank ID GI Number Organism Gfa Q51669.3 38257308 Paracoccus denitrificans Gfa ABP71667.1 145557054 Rhodobacter sphaeroides ATCC 17025 Gfa Q92WX6.1 38257348 Sinorhizobium meliloti 1021 Gfa Q98LU4.2 38257349 Mesorhizobium loti MAFF303099

FIG. 4, Step N—Glutathione-Dependent Formaldehyde Dehydrogenase

Glutathione-dependent formaldehyde dehydrogenase (GS-FDH) belongs to the family of class III alcohol dehydrogenases. Glutathione and formaldehyde combine non-enzymatically to form hydroxymethylglutathione, the true substrate of the GS-FDH catalyzed reaction. The product, S-formylglutathione, is further metabolized to formic acid.

Protein GenBank ID GI Number Organism frmA YP_488650.1 388476464 Escherichia coli K-12 MG1655 SFA1 NP010113.1 6320033 Saccharomyces cerevisiae S288c flhA AAC44551.1 1002865 Paracoccus denitrificans adhI AAB09774.1 986949 Rhodobacter sphaeroides

FIG. 4, Step O—S-Formylglutathione Hydrolase

S-formylglutathione hydrolase is a glutathione thiol esterase found in bacteria, plants and animals. It catalyzes conversion of S-formylglutathione to formate and glutathione. The fghA gene of P. denitfrifcans is located in the same operon with gfa and flhA, two genes involved in the oxidation of formaldehyde to formate in this organism. In E. coli, FrmB is encoded in an operon with FrmR and FrmA, which are proteins involved in the oxidation of formaldehyde. YeiG of E. coli is a promiscuous serine hydrolase; its highest specific activity is with the substrate S-formylglutathione.

Protein GenBank ID GI Number Organism frmB NP_414889.1 16128340 Escherichia coli K-12 MG1655 yeiG AAC75215.1 1788477 Escherichia coli K-12 MG1655 fghA AAC44554.1 1002868 Paracoccus denitrificans

FIG. 4, Step P—Carbon Monoxide Dehydrogenase (CODH)

CODH is a reversible enzyme that interconverts CO and CO₂ at the expense or gain of electrons. The natural physiological role of the CODH in ACS/CODH complexes is to convert CO₂ to CO for incorporation into acetyl-CoA by acetyl-CoA synthase. Nevertheless, such CODH enzymes are suitable for the extraction of reducing equivalents from CO due to the reversible nature of such enzymes. Expressing such CODH enzymes in the absence of ACS allows them to operate in the direction opposite to their natural physiological role (i.e., CO oxidation).

In M. thermoacetica, C. hydrogenoformans, C. carboxidivorans P7, and several other organisms, additional CODH encoding genes are located outside of the ACS/CODH operons. These enzymes provide a means for extracting electrons (or reducing equivalents) from the conversion of carbon monoxide to carbon dioxide. The M. thermoacetica gene (Genbank Accession Number: YP_430813) is expressed by itself in an operon and is believed to transfer electrons from CO to an external mediator like ferredoxin in a “Ping-pong” reaction. The reduced mediator then couples to other reduced nicolinamide adenine dinucleotide phosphate (NAD(P)H) carriers or ferredoxin-dependent cellular processes (Ragsdale, Annals of the New York Academy of Sciences 1125: 129-136 (2008)). The genes encoding the C. hydrogenoformans CODH-II and CooF, a neighboring protein, were cloned and sequenced (Gonzalez and Robb, FEMS Microbiol Lett. 191:243-247 (2000)). The resulting complex was membrane-bound, although cytoplasmic fractions of CODH-II were shown to catalyze the formation of NADPH suggesting an anabolic role (Svetlitchnyi et al., J Bacteriol. 183:5134-5144 (2001)). The crystal structure of the CODH-II is also available (Dobbek et al., Science 293:1281-1285 (2001)). Similar ACS-free CODH enzymes can be found in a diverse array of organisms including Geobacter metallireducens GS-15, Chlorobium phaeobacteroides DSM 266, Clostridium cellulolyticum H10, Desulfovibrio desulfitricans subsp. desulfitricans str. ATCC 27774, Pelobacter carbinolicus DSM 2380, C. ljungdahli and Campylobacter curvus 525.92.

Protein GenBank ID GI Number Organism CODH (putative) YP_430813 83590804 Moorella thermoacetica CODH-II (CooS-II) YP_358957 78044574 Carboxydothermus hydrogenoformans CooF YP_358958 78045112 Carboxydothermus hydrogenoformans CODH (putative) ZP_05390164.1 255523193 Clostridium carboxidivorans P7 CcarbDRAFT_0341 ZP_05390341.1 255523371 Clostridium carboxidivorans P7 CcarbDRAFT_1756 ZP_05391756.1 255524806 Clostridium carboxidivorans P7 CcarbDRAFT_2944 ZP_05392944.1 255526020 Clostridium carboxidivorans P7 CODH YP_384856.1 78223109 Geobacter metallireducens GS-15 Cpha266 0148 (cytochrome c) YP_910642.1 119355998 Chlorobium phaeobacteroides DSM 266 Cpha266 0149 (CODH) YP_910643.1 119355999 Chlorobium phaeobacteroides DSM 266 Ccel 0438 YP_002504800.1 220927891 Clostridium cellulolyticum H10 Ddes_0382 (CODH) YP_002478973.1 220903661 Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Ddes_0381 (CooC) YP_002478972.1 220903660 Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774 Pcar_0057 (CODH) YP_355490.1 7791767 Pelobacter carbinolicus DSM 2380 Pcar_0058 (CooC) YP_355491.1 7791766 Pelobacter carbinolicus DSM 2380 Pcar_0058 (HypA) YP_355492.1 7791765 Pelobacter carbinolicus DSM 2380 CooS(CODH) YP_001407343.1 154175407 Campylobacter curvus 525.92 CUU c09110 ADK13979.1 300434212 Clostridium ljungdahli CUU_c09100 ADK13978.1 300434211 Clostridium ljungdahli CUU_c09090 ADK13977.1 300434210 Clostridium ljungdahli

Example V Methods for Formaldehyde Fixation

Provided herein are exemplary pathways, which utilize formaldehyde produced from the oxidation of methanol (see, e.g., FIG. 3, step A, or FIG. 4, step J) or from formate assimilation pathways described in Example III (see, e.g., FIG. 3) in the formation of intermediates of certain central metabolic pathways that can be used for the production of compounds disclosed herein.

One exemplary pathway that can utilize formaldehyde produced from the oxidation of methanol is shown in FIG. 3, which involves condensation of formaldehyde and D-ribulose-5-phosphate to form hexulose-6-phosphate (h6p) by hexulose-6-phosphate synthase (FIG. 3, step B). The enzyme can use Mg²⁺ or Mn²⁺ for maximal activity, although other metal ions are useful, and even non-metal-ion-dependent mechanisms are contemplated. H6p is converted into fructose-6-phosphate by 6-phospho-3-hexuloisomerase (FIG. 3, step C).

Another exemplary pathway that involves the detoxification and assimilation of formaldehyde produced from the oxidation of methanol is shown in FIG. 3 and proceeds through dihydroxyacetone. Dihydroxyacetone synthase is a special transketolase that first transfers a glycoaldehyde group from xylulose-5-phosphate to formaldehyde, resulting in the formation of dihydroxyacetone (DHA) and glyceraldehyde-3-phosphate (G3P), which is an intermediate in glycolysis (FIG. 3). The DHA obtained from DHA synthase can be further phosphorylated to form DHA phosphate and assimilated into glycolysis and several other pathways (FIG. 3). Alternatively, or in addition, a fructose-6-phosphate aldolase can be used to catalyze the conversion of DHA and G3P to fructose-6-phosphate (FIG. 3, step Z).

FIG. 3, Steps B and C—Hexulose-6-Phosphate Synthase (Step B) and 6-Phospho-3-Hexuloisomerase (Step C)

Both of the hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase enzymes are found in several organisms, including methanotrophs and methylotrophs where they have been purified (Kato et al., 2006, BioSci Biotechnol Biochem. 70(1):10-21. In addition, these enzymes have been reported in heterotrophs such as Bacillus subtilis also where they are reported to be involved in formaldehyde detoxification (Mitsui et al., 2003, AEM 69(10):6128-32, Yasueda et al., 1999. J Bac 181(23):7154-60. Genes for these two enzymes from the methylotrophic bacterium Mycobacterium gastri MB19 have been fused and E. coli strains harboring the hps-phi construct showed more efficient utilization of formaldehyde (Orita et al., 2007, Appl Microbiol Biotechnol. 76:439-445). In some organisms, these two enzymes naturally exist as a fused version that is bifunctional.

Exemplary candidate genes for hexulose-6-phosphate synthase are:

Protein GenBank ID GI number Organism Hps AAR39392.1 40074227 Bacillus methanolicus MGA3 Hps EIJ81375.1 387589055 Bacillus methanolicus PB1 RmpA BAA83096.1 5706381 Methylomonas aminofaciens RmpA BAA90546.1 6899861 Mycobacterium gastri YckG BAA08980.1 1805418 Bacillus subtilis Hps YP_544362.1 91774606 Methylobacillus flagellatus Hps YP_545763.1 91776007 Methylobacillus flagellatus Hps AAG29505.1 11093955 Aminomonas aminovorus SgbH YP_004038706.1 313200048 Methylovorus sp. MP688 Hps YP_003050044.1 253997981 Methylovorus glucosetrophus SIP3-4 Hps YP_003990382.1 312112066 Geobacillus sp. Y4.1MC1 Hps gb|AAR91478.1 40795504 Geobacillus sp. M10EXG Hps YP_007402409.1 448238351 Geobacillus sp. GHH01

Exemplary gene candidates for 6-phospho-3-hexuloisomerase are:

Protein GenBank ID GI number Organism Phi AAR39393.1 40074228 Bacillus methanolicus MGA3 Phi EIJ81376.1 387589056 Bacillus methanolicus PB1 Phi BAA83098.1 5706383 Methylomonas aminofaciens RmpB BAA90545.1 6899860 Mycobacterium gastri Phi YP_545762.1 91776006 Methylobacillus flagellatus KT Phi YP_003051269.1 253999206 Methylovorus glucosetrophus SIP3-4 Phi YP_003990383.1 312112067 Geobacillus sp. Y4.1MC1 Phi YP_007402408.1 448238350 Geobacillus sp. GHH01

Candidates for enzymes where both of these functions have been fused into a single open reading frame include the following.

Protein GenBank ID GI number Organism PH1938 NP_143767.1 14591680 Pyrococcus horikoshii OT3 PF0220 NP_577949.1 18976592 Pyrococcus furiosus TK0475 YP_182888.1 57640410 Thermococcus kodakaraensis PAB1222 NP_127388.1 14521911 Pyrococcus abyssi MCA2738 YP_115138.1 53803128 Methylococcus capsulatas Metal_3152 EIC30826.1 380884949 Methylomicrobium album BG8

FIG. 3, Step D—Dihydroxyacetone Synthase

The dihydroxyacetone synthase enzyme in Candida boidinii uses thiamine pyrophosphate and Mg²⁺ as cofactors and is localized in the peroxisome. The enzyme from the methanol-growing carboxydobacterium, Mycobacter sp. strain JC1 DSM 3803, was also found to have DHA synthase and kinase activities (Ro et al., 1997, JBac 179(19):6041-7). DHA synthase from this organism also has similar cofactor requirements as the enzyme from C. boidinii. The K_(m)s for formaldehyde and xylulose 5-phosphate were reported to be 1.86 mM and 33.3 microM, respectively. Several other mycobacteria, excluding only Mycobacterium tuberculosis, can use methanol as the sole source of carbon and energy and are reported to use dihydroxyacetone synthase (Part et al., 2003, JBac 185(1):142-7.

Protein GenBank ID GI number Organism DAS1 AAC83349.1 3978466 Candida boidinii HPODL_2613 EFW95760.1 320581540 Ogataea parapolymorpha DL-1 (Hansenula polymorpha DL-1) AAG12171.2 18497328 Mycobacter sp. strain JC1 DSM 3803

FIG. 3, Step Z—Fructose-6-Phosphate Aldolase

Fructose-6-phosphate aldolase (F6P aldolase) can catalyze the combination of dihydroxyacetone (DHA) and glyceraldehyde-3-phosphate (G3P) to form fructose-6-phosphate. This activity was recently discovered in E. coli and the corresponding gene candidate has been termed fsa (Schurmann and Sprenger, J Biol. Chem., 2001, 276(14), 11055-11061). The enzyme has narrow substrate specificity and cannot utilize fructose, fructose 1-phosphate, fructose 1,6-bisphosphate, or dihydroxyacetone phosphate. It can however use hydroxybutanone and acetol instead of DHA. The purified enzyme displayed a V_(max) of 7 units/mg of protein for fructose 6-phosphate cleavage (at 30 degrees C., pH 8.5 in 50 mm glycylglycine buffer). For the aldolization reaction a V_(max) of 45 units/mg of protein was found; K_(m) values for the substrates were 9 mM for fructose 6-phosphate, 35 mM for dihydroxyacetone, and 0.8 mM for glyceraldehyde 3-phosphate. The enzyme prefers the aldol formation over the cleavage reaction.

The selectivity of the E. coli enzyme towards DHA can be improved by introducing point mutations. For example, the mutation A129S improved reactivity towards DHA by over 17 fold in terms of K_(cat)/K_(m)(Gutierrez et al., Chem Commun (Camb), 2011, 47(20), 5762-5764). The same mutation reduced the catalytic efficiency on hydroxyacetone by more than 3 fold and reduced the affinity for glycoaldehyde by more than 3 fold compared to that of the wild type enzyme (Castillo et al., Advanced Synthesis & Catalysis, 352(6), 1039-1046). Genes similar to fsa have been found in other genomes by sequence homology. Some exemplary gene candidates have been listed below.

Gene Protein accession no. GI number Organism fsa AAC73912.2 87081788 Escherichia coli K12 talC AAC76928.1 1790382 Escherichia coli K12 fsa WP_017209835.1 515777235 Clostridium beijerinckii DR 1337 AAF10909.1 6459090 Deinococcus radiodurans R1 talC NP_213080.1 15605703 Aquifex aeolicus VF5 MJ_0960 NP_247955.1 15669150 Methanocaldococcus janaschii mipB NP_993370.2 161511381 Yersinia pestis

As Described Below, there is an Energetic Advantage to Using F6P Aldolase in the DHA Pathway.

The assimilation of formaldehyde formed by the oxidation of methanol can proceed either via the dihydroxyacetone (DHA) pathway (step D, FIG. 3) or the Ribulose monophosphate (RuMP) pathway (steps B and C, FIG. 3). In the RuMP pathway, formaldehyde combines with ribulose-5-phosphate to form F6P. F6P is then either metabolized via glycolysis or used for regeneration of ribulose-5-phosphate to enable further formaldehyde assimilation. Notably, ATP hydrolysis is not required to form F6P from formaldehyde and ribulose-5-phosphate via the RuMP pathway.

In contrast, in the DHA pathway, formaldehyde combines with xylulose-5-phosphate (X5P) to form dihydroxyacetone (DHA) and glyceraldehyde-3-phosphate (G3P). Some of the DHA and G3P must be metabolized to F6P to enable regeneration of xylulose-5-phosphate. In the standard DHA pathway, DHA and G3P are converted to F6P by three enzymes: DHA kinase, fructose bisphosphate aldolase, and fructose bisphosphatase. The net conversion of DHA and G3P to F6P requires ATP hydrolysis as described below. First, DHA is phosphorylated to form DHA phosphate (DHAP) by DHA kinase at the expense of an ATP. DHAP and G3P are then combined by fructose bisphosphate aldolase to form fructose-1,6-diphosphate (FDP). FDP is converted to F6P by fructose bisphosphatase, thus wasting a high energy phosphate bond.

A more ATP efficient sequence of reactions is enabled if DHA synthase functions in combination with F6P aldolase as opposed to in combination with DHA kinase, fructose bisphosphate aldolase, and fructose bisphosphatase. F6P aldolase enables direct conversion of DHA and G3P to F6P, bypassing the need for ATP hydrolysis. Overall, DHA synthase when combined with F6P aldolase is identical in energy demand to the RuMP pathway. Both of these formaldehyde assimilation options (i.e., RuMP pathway, DHA synthase+F6P aldolase) are superior to DHA synthase combined with DHA kinase, fructose bisphosphate aldolase, and fructose bisphosphatase in terms of ATP demand.

Example VI Phosphoketolase-Dependent Acetyl-CoA Synthesis Enzymes

This Example provides genes that can be used for enhancing carbon flux through acetyl-CoA using phosphoketolase enzymes.

FIG. 3, Step T—Fructose-6-Phosphate Phosphoketolase

Conversion of fructose-6-phosphate and phosphate to acetyl-phosphate and erythrose-5-phosphate can be carried out by fructose-6-phosphate phosphoketolase (EC 4.1.2.22). Conversion of fructose-6-phosphate and phosphate to acetyl-phosphate and erythrose-5-phosphate is one of the key reactions in the Bifidobacterium shunt. There is evidence for the existence of two distinct phosphoketolase enzymes in bifidobacteria (Sgorbati et al, 1976, Antonie Van Leeuwenhoek, 42(1-2) 49-57; Grill et al, 1995, Curr Microbiol, 31(0; 49-54). The enzyme from Bifidobacterium dentium appeared to be specific solely for fructose-6-phosphate (EC: 4.1.2.22) while the enzyme from Bifidobacterium pseudolongum subsp. globosum is able to utilize both fructose-6-phosphate and D-xylulose 5-phosphate (EC: 4.1.2.9) (Sgorbati et al, 1976, Antonie Van Leeuwenhoek, 42(1-2) 49-57). The enzyme encoded by the xfp gene, originally discovered in Bifidobacterium animal's lactis, is the dual-specificity enzyme (Meile et al., 2001, J. Bacteriol, 183, 2929-2936; Yin et al, 2005, FEMS Microbiol Lett, 246(2); 251-257). Additional phosphoketolase enzymes can be found in Leuconostoc mesenteroides (Lee et al, Biotechnol Lett. 2005 June; 27(12):853-8), Clostridium acetobutylicum ATCC 824 (Servinsky et al, Journal of Industrial Microbiology & Biotechnology, 2012, 39, 1859-1867), Aspergillus nidulans (Kocharin et al, 2013, Biotechnol Bioeng, 110(8), 2216-2224; Papini, 2012, Appl Microbiol Biotechnol, 95 (4), 1001-1010), Bifidobacterium breve (Suziki et al, 2010, Acta Crystallogr Sect F Struct Biol Cryst Commun., 66(Pt 8):941-3), Lactobacillus paraplantarum (Jeong et al, 2007, J Microbiol Biotechnol, 17(5), 822-9).

Protein GENBANK ID GI NUMBER ORGANISM xfp YP_006280131.1 386867137 Bifidobacterium animalis lactis xfp AAV66077.1 55818565 Leuconostoc mesenteroides CAC1343 NP_347971.1 15894622 Clostridium acetobutylicum ATCC 824 xpkA CBF76492.1 259482219 Aspergillus nidulans xfp WP_003840380.1 489937073 Bifidobacterium dentium ATCC 27678 xfp AAR98788.1 41056827 Bifidobacterium pseudolongum subsp. globosum xfp WP_022857642.1 551237197 Bifidobacterium pseudolongum subsp. globosum xfp ADF97524.1 295314695 Bifidobacterium breve xfp AAQ64626.1 34333987 Lactobacillus paraplantarum

FIG. 3, Step U—Xylulose-5-Phosphate Phosphoketolase

Conversion of xylulose-5-phosphate and phosphate to acetyl-phosphate and glyceraldehyde-3-phosphate can be carried out by xylulose-5-phosphate phosphoketolase (EC 4.1.2.9). There is evidence for the existence of two distinct phosphoketolase enzymes in bifidobacteria (Sgorbati et al, 1976, Antonie Van Leeuwenhoek, 42(1-2) 49-57; Grill et al, 1995, Curr Microbiol, 31(0; 49-54). The enzyme from Bifidobacterium dentium appeared to be specific solely for fructose-6-phosphate (EC: 4.1.2.22) while the enzyme from Bifidobacterium pseudolongum subsp. globosum is able to utilize both fructose-6-phosphate and D-xylulose 5-phosphate (EC: 4.1.2.9) (Sgorbati et al, 1976, Antonie Van Leeuwenhoek, 42(1-2) 49-57). Many characterized enzymes have dual-specificity for xylulose-5-phosphate and fructose-6-phosphate. The enzyme encoded by the xfp gene, originally discovered in Bifidobacterium animal's lactis, is the dual-specificity enzyme (Meile et al., 2001, J. Bacteriol, 183, 2929-2936; Yin et al, 2005, FEMS Microbiol Lett, 246(2); 251-257). Additional phosphoketolase enzymes can be found in Leuconostoc mesenteroides (Lee et al, Biotechnol Let 2005 June; 27(12):853-8), Clostridium acetobutylicum ATCC 824 (Servinsky et al, Journal of Industrial Microbiology & Biotechnology, 2012, 39, 1859-1867), Aspergillus nidulans (Kocharin et al, 2013, Biotechnol Bioeng, 110(8), 2216-2224; Papini, 2012, Appl Microbiol Biotechnol, 95 (4), 1001-1010), Bifidobacterium breve (Suziki et al, 2010, Acta Crystallogr Sect F Struct Biol Cryst Commun., 66(Pt 8):941-3), and Lactobacillus paraplantarum (Jeong et al, 2007, J Microbiol Biotechnol, 17(5), 822-9).

Protein GENBANK ID GI NUMBER ORGANISM xfp YP_006280131.1 386867137 Bifidobacterium animalis lactis xfp AAV66077.1 55818565 Leuconostoc mesenteroides CAC1343 NP_347971.1 15894622 Clostridium acetobutylicum ATCC 824 xpkA CBF76492.1 259482219 Aspergillus nidulans xfp AAR98788.1 41056827 Bifidobacterium pseudolongum subsp. globosum xfp WP_022857642.1 551237197 Bifidobacterium pseudolongum subsp. globosum xfp ADF97524.1 295314695 Bifidobacterium breve xfp AAQ64626.1 34333987 Lactobacillus paraplantarum

FIG. 3, Step V—Phosphotransacetylase

The formation of acetyl-CoA from acetyl-phosphate can be catalyzed by phosphotransacetylase (EC 2.3.1.8). The pta gene from E. coli encodes an enzyme that reversibly converts acetyl-CoA into acetyl-phosphate (Suzuki, T., Biochim. Biophys. Acta 191:559-569 (969)). Additional acetyltransferase enzymes have been characterized in Bacillus subtilis (Rado and Hoch, Biochim. Biophys. Acta 321:114-125 (1973), Clostridium kluyveri (Stadtman, E., Methods Enzymol. 1:5896-599 (1955), and Thermotoga maritima (Bock et al., J. Bacteriol. 181:1861-1867 (1999)). This reaction can also be catalyzed by some phosphotransbutyrylase enzymes (EC 2.3.1.19), including the ptb gene products from Clostridium acetobutylicum (Wiesenbom et al., App. Environ. Microbiol. 55:317-322 (1989); Walter et al., Gene 134:107-111 (1993)). Additional ptb genes are found in butyrate-producing bacterium L2-50 (Louis et al., J. Bacteriol. 186:2099-2106 (2004) and Bacillus megaterium (Vazquez et al., Curr. Microbiol. 42:345-349 (2001). Homologs to the E. coli pta gene exist in several other organisms including Salmonella enterica and Chlamydomonas reinhardtii.

Protein GenBank ID GI Number Organism Pta NP_416800.1 71152910 Escherichia coli Pta P39646 730415 Bacillus subtilis Pta A5N801 146346896 Clostridium kluyveri Pta Q9X0L4 6685776 Thermotoga maritime Ptb NP_349676 34540484 Clostridium acetobutylicum Ptb AAR19757.1 38425288 butyrate-producing bacterium L2-50 Ptb CAC07932.1 10046659 Bacillus megaterium Pta NP_461280.1 16765665 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 PAT2 XP_001694504.1 159472743 Chlamydomonas reinhardtii PAT1 XP_001691787.1 159467202 Chlamydomonas reinhardtii

FIG. 3, Step W—Acetate Kinase

Acetate kinase (EC 2.7.2.1) can catalyze the reversible ATP-dependent phosphorylation of acetate to acetylphosphate. Exemplary acetate kinase enzymes have been characterized in many organisms including E. coli, Clostridium acetobutylicum and Methanosarcina thermophila (Ingram-Smith et al., J. Bacteriol. 187:2386-2394 (2005); Fox and Roseman, J. Biol. Chem. 261:13487-13497 (1986); Winzer et al., Microbiology 143 (Pt 10):3279-3286 (1997)). Acetate kinase activity has also been demonstrated in the gene product of E. coli purT (Marolewski et al., Biochemistry 33:2531-2537 (1994). Some butyrate kinase enzymes (EC 2.7.2.7), for example buk1 and buk2 from Clostridium acetobutylicum, also accept acetate as a substrate (Hartmanis, M. G., J. Biol. Chem. 262:617-621 (1987)). Homologs exist in several other organisms including Salmonella enterica and Chlamydomonas reinhardtii.

Protein GenBank ID GI Number Organism ackA NP_416799.1 16130231 Escherichia coli Ack AAB18301.1 1491790 Clostridium acetobutylicum Ack AAA72042.1 349834 Methanosarcina thermophila purT AAC74919.1 1788155 Escherichia coli buk1 NP_349675 15896326 Clostridium acetobutylicum buk2 Q97II1 20137415 Clostridium acetobutylicum ackA NP_461279.1 16765664 Salmonella typhimurium ACK1 XP_001694505.1 159472745 Chlamydomonas reinhardtii ACK2 XP_001691682.1 159466992 Chlamydomonas reinhardtii

FIG. 3, Step X—Acetyl-CoA Transferase, Synthetase, or Ligase

The acylation of acetate to acetyl-CoA can be catalyzed by enzymes with acetyl-CoA synthetase, ligase or transferase activity. Two enzymes that can catalyze this reaction are AMP-forming acetyl-CoA synthetase or ligase (EC 6.2.1.1) and ADP-forming acetyl-CoA synthetase (EC 6.2.1.13). AMP-forming acetyl-CoA synthetase (ACS) is the predominant enzyme for activation of acetate to acetyl-CoA. Exemplary ACS enzymes are found in E. coli (Brown et al., J. Gen. Microbiol. 102:327-336 (1977)), Ralstonia eutropha (Priefert and Steinbuchel, J. Bacteriol. 174:6590-6599 (1992)), Methanothermobacter thermautotrophicus (Ingram-Smith and Smith, Archaea 2:95-107 (2007)), Salmonella enterica (Gulick et al., Biochemistry 42:2866-2873 (2003)) and Saccharomyces cerevisiae (Jogl and Tong, Biochemistry 43:1425-1431(2004)). ADP-forming acetyl-CoA synthetases are reversible enzymes with a generally broad substrate range (Musfeldt and Schonheit, J. Bacteriol. 184:636-644 (2002)). Two isozymes of ADP-forming acetyl-CoA synthetases are encoded in the Archaeoglobus fulgidus genome by are encoded by AF1211 and AF1983 (Musfeldt and Schonheit, supra (2002)). The enzyme from Haloarcula marismortui (annotated as a succinyl-CoA synthetase) also accepts acetate as a substrate and reversibility of the enzyme was demonstrated (Brasen and Schonheit, Arch. Microbiol. 182:277-287 (2004)). The ACD encoded by PAE3250 from hyperthermophilic crenarchaeon Pyrobaculum aerophilum showed the broadest substrate range of all characterized ACDs, reacting with acetate, isobutyryl-CoA (preferred substrate) and phenylacetyl-CoA (Brasen and Schonheit, supra (2004)). Directed evolution or engineering can be used to modify this enzyme to operate at the physiological temperature of the host organism. The enzymes from A. fulgidus, H. marismortui and P. aerophilum have all been cloned, functionally expressed, and characterized in E. coli (Brasen and Schonheit, supra (2004); Musfeldt and Schonheit, supra (2002)). Additional candidates include the succinyl-CoA synthetase encoded by sucCD in E. coli (Buck et al., Biochemistry 24:6245-6252 (1985)) and the acyl-CoA ligase from Pseudomonas putida (Femandez-Valverde et al., Appl. Environ. Microbiol. 59:1149-1154 (1993)). The aforementioned proteins are shown below.

Protein Gen Bank ID GI Number Organism Acs AAC77039.1 1790505 Escherichia coli acoE AAA21945.1 141890 Ralstonia eutropha acs1 ABC87079.1 86169671 Methanothermobacter thermautotrophicus acs1 AAL23099.1 16422835 Salmonella enterica ACS1 Q01574.2 257050994 Saccharomyces cerevisiae AF1211 NP_070039.1 11498810 Archaeoglobus fulgidus AF1983 NP_070807.1 11499565 Archaeoglobus fulgidus Scs YP_135572.1 55377722 Haloarcula marismortui PAE3250 NP_560604.1 18313937 Pyrobaculum aerophilum str. IM2 sucC NP_415256.1 16128703 Escherichia coli sucD AAC73823.1 1786949 Escherichia coli paaF AAC24333.2 22711873 Pseudomonas putida

An acetyl-CoA transferase that can utilize acetate as the CoA acceptor is acetoacetyl-CoA transferase, encoded by the E. coli atoA (alpha subunit) and atoD (beta subunit) genes (Vanderwinkel et al., Biochem. Biophys. Res Commun. 33:902-908 (1968); Korolev et al., Acta Crystallogr. D Biol Crystallogr. 58:2116-2121(2002)). This enzyme has also been shown to transfer the CoA moiety to acetate from a variety of branched and linear acyl-CoA substrates, including isobutyrate (Matthies et al., Appl Environ Microbiol 58:1435-1439 (1992)), valerate (Vanderwinkel et al., supra) and butanoate (Vanderwinkel et al., supra). Similar enzymes exist in Corynebacterium glutamicum ATCC 13032 (Duncan et al., Appl Environ Microbiol 68:5186-5190 (2002)), Clostridium acetobutylicum (Cary et al., Appl Environ Microbiol 56:1576-1583 (1990)), and Clostridium saccharoperbutylacetonicum (Kosaka et al., Biosci. Biotechnol Biochem. 71:58-68 (2007)). These proteins are identified below.

Protein Gen Bank ID GI Number Organism atoA P76459.1 2492994 Escherichia coli K12 atoD P76458.1 2492990 Escherichia coli K12 actA YP_226809.1 62391407 Corynebacterium glutamicum ATCC 13032 cg0592 YP_224801.1 62389399 Corynebacterium glutamicum ATCC 13032 ctfA NP_149326.1 15004866 Clostridium acetobutylicum ctfB NP_149327.1 15004867 Clostridium acetobutylicum ctfA AAP42564.1 31075384 Clostridium saccharoperbutylacetonicum ctfB AAP42565.1 31075385 Clostridium saccharoperbutylacetonicum

Additional exemplary acetyl-CoA transferase candidates are catalyzed by the gene products of cat1, cat2, and cat3 of Clostridium kluyveri which have been shown to exhibit succinyl-CoA, 4-hydroxybutyryl-CoA, and butyryl-CoA transferase activity, respectively (Seedorf et al., supra; Sohling et al., Eur. J Biochem. 212:121-127 (1993); Sohling et al., J. Bacteriol. 178:871-880 (1996)). Similar CoA transferase activities are also present in Trichomonas vaginalis (van Grinsven et al., J. Biol. Chem. 283:1411-1418 (2008)) and Trypanosoma brucei (Riviere et al., J. Biol. Chem. 279:45337-45346 (2004)). These proteins are identified below.

Protein GenBank ID GI Number Organism cat1 P38946.1 729048 Clostridium kluyveri cat2 P38942.2 172046066 Clostridium kluyveri cat3 EDK35586.1 146349050 Clostridium kluyveri TVAG_395550 XP_001330176 123975034 Trichomonas vaginalis G3 Tb11.02.0290 XP_828352 71754875 Trypanosoma brucei

Example VII Attenuation or Disruption of Endogenous Enzymes

This example provides endogenous enzyme targets for attenuation or disruption that can be used for enhancing carbon flux through acetyl-CoA.

DHA Kinase

Methylotrophic yeasts typically utilize a cytosolic DHA kinase to catalyze the ATP-dependent activation of DHA to DHAP. DHAP together with G3P is combined to form fructose-1,6-bisphosphate (FBP) by FBP aldolase. FBP is then hydrolyzed to F6P by fructose bisphosphatase. The net conversion of DHA and G3P to F6P by this route is energetically costly (1 ATP) in comparison to the F6P aldolase route, described above and shown in FIG. 3. DHA kinase also competes with F6P aldolase for the DHA substrate. Attenuation of endogenous DHA kinase activity will thus improve the energetics of formaldehyde assimilation pathways, and also increase the intracellular availability of DHA for DHA synthase. DHA kinases of Saccharomyces cerevisiae, encoded by DAK1 and DAK2, enable the organism to maintain low intracellular levels of DHA (Molin et al, J Biol Chem 278:1415-23 (2003)). In methylotrophic yeasts DHA kinase is essential for growth on methanol (Luers et al, Yeast 14:759-71 (1998)). The DHA kinase enzymes of Hansenula polymorpha and Pichia pastoris are encoded by DAK (van der Klei et al, Curr Genet 34:1-11(1998); Luers et al, supra). DAK enzymes in other organisms can be identified by sequence similarity to known enzymes.

Protein GenBank ID GI Number Organism DAK1 NP_013641.1 6323570 Saccharomyces cerevisiae DAK2 NP_116602.1 14318466 Saccharomyces cerevisiae DAK AAC27705.1 3171001 Hansenula polymorpha DAK AAC39490.1 3287486 Pichia pastoris DAK2 XP_505199.1 50555582 Yarrowia lipolytica Methanol Oxidase

Attenuation of redox-inefficient endogenous methanol oxidizing enzymes, combined with increased expression of a cytosolic NADH-dependent MeDH, will enable redox-efficient oxidation of methanol to formaldehyde in the cytosol. Methanol oxidase, also called alcohol oxidase (EC 1.1.3.13), catalyzes the oxygen-dependent oxidation of methanol to formaldehyde and hydrogen peroxide. In eukaryotic organisms, alcohol oxidase is localized in the peroxisome. Exemplary methanol oxidase enzymes are encoded by AOD of Candida boidinii (Sakai and Tani, Gene 114:67-73 (1992)); and AOX of H. polymorpha, P. methanolica and P. pastoris (Ledeboer et al, Nucl Ac Res 13:3063-82 (1985); Koutz et al, Yeast 5:167-77 (1989); Nakagawa et al, Yeast 15:1223-1230 (1999)).

Protein GenBank ID GI Number Organism AOX2 AAF02495.1 6049184 Pichia methanolica AOX1 AAF02494.1 6049182 Pichia methanolica AOX1 AAB57849.1 2104961 Pichia pastoris AOX2 AAB57850.1 2104963 Pichia pastoris AOX P04841.1 113652 Hansenula polymorpha AOD1 Q00922.1 231528 Candida boidinii AOX1 AAQ99151.1 37694459 Ogataea pini PQQ-Dependent MeDH

PQQ-dependent MeDH from M. extorquens (mxaIF) uses cytochrome as an electron carrier (Nunn et al, Nucl Acid Res 16:7722 (1988)). MeDH enzymes of methanotrophs such as Methylococcus capsulatis function in a complex with methane monooxygenase (MMO) (Myronova et al, Biochem 45:11905-14 (2006)). Note that of accessory proteins, cytochrome CL and PQQ biosynthesis enzymes are needed for active MeDH. Attenuation of one or more of these required accessory proteins, or retargeting the enzyme to a different cellular compartment, would also have the effect of attenuating PQQ-dependent MeDHactivity.

Protein GenBank ID GI Number Organism MCA0299 YP_112833.1 53802410 Methylococcus capsulatis MCA0782 YP_113284.1 53804880 Methylococcus capsulatis mxaI YP_002965443.1 240140963 Methylobacterium extorquens mxaF YP_002965446.1 240140966 Methylobacterium extorquens DHA Synthase and Other Competing Formaldehyde Assimilation and Dissimilation Pathways

Carbon-efficient formaldehyde assimilation can be improved by attenuation of competing formaldehyde assimilation and dissimilation pathways. Exemplary competing assimilation pathways in eukaryotic organisms include the peroxisomal dissimilation of formaldehyde by DHA synthase, and the DHA kinase pathway for converting DHA to F6P, both described herein. Exemplary competing endogenous dissimilation pathways include one or more of the enzymes shown in FIG. 3.

Methylotrophic yeasts normally target selected methanol assimilation and dissimilation enzymes to peroxisomes during growth on methanol, including methanol oxidase, DHA synthase and S-(hydroxymethyl)-glutathione synthase (see review by Yurimoto et al, supra). The peroxisomal targeting mechanism comprises an interaction between the peroxisomal targeting sequence and its corresponding peroxisomal receptor (Lametschwandtner et al, J Biol Chem 273:33635-43 (1998)). Peroxisomal methanol pathway enzymes in methylotrophic organisms contain a PTS1 targeting sequence which binds to a peroxisomal receptor, such as Pex5p in Candida boidinii (Horiguchi et al, J. Bacteriol 183:6372-83 (2001)). Disruption of the PTS1 targeting sequence, the Pex5p receptor and/or genes involved in peroxisomal biogenesis would enable cytosolic expression of DHA synthase, S-(hydroxymethyl)-glutathione synthase or other methanol-inducible peroxisomal enzymes. PTS1 targeting sequences of methylotrophic yeast are known in the art (Horiguchi et al, supra). Identification of peroxisomal targeting sequences of unknown enzymes can be predicted using bioinformatic methods (eg. Neuberger et al, J Mol Biol 328:581-92 (2003))).

Example VIII Methanol Assimilation Via MeDH and the Ribulose Monophosphate Pathway

This example shows that co-expression of an active MeDH(MeDH) and the enzymes of the Ribulose Monophosphate (RuMP) pathway can effectively assimilate methanol derived carbon.

An experimental system was designed to test the ability of a MeDH in conjunction with the enzymes H6P synthase (HPS) and 6P3E11 (PHI) of the RuMP pathway to assimilate methanol carbon into the glycolytic pathway and the TCA cycle. Escherichia coli strain ECh-7150 (ΔlacIA, ΔpflB, ΔptsI, ΔPpckA(pckA), ΔPglk(glk), glk::glfB, ΔhycE, ΔfrmR, ΔfrmA, ΔfrmB) was constructed to remove the glutathione-dependent formaldehyde detoxification capability encoded by the FrmA and FrmB enzyme. This strain was then transformed with plasmid pZA23S variants that either contained or lacked gene 2616A encoding a fusion of the HPS and PHI enzymes. These two transformed strains were then each transformed with pZS*13S variants that contained gene 2315L (encoding an active MeDH), or gene 2315 RIP2 (encoding a catalytically inactive MeDH), or no gene insertion. Genes 2315 and 2616 are internal nomenclatures for NAD-dependent MeDH from Bacillus methanolicus MGA3 and 2616 is a fused phs-hpi constructs as described in Orita et al. (2007) Appl Microbiol Biotechnol 76:439-45.

The six resulting strains were aerobically cultured in quadruplicate, in 5 ml minimal medium containing 1% arabinose and 0.6 M 13C-methanol as well as 100 ug/ml carbenicillin and 25 μg/ml kanamycin to maintain selection of the plasmids, and 1 mM IPTG to induce expression of the MeDH and HPS-PHI fusion enzymes. After 18 hours incubation at 37° C., the cell density was measured spectrophotometrically at 600 nM wavelength and a clarified sample of each culture medium was submitted for analysis to detect evidence of incorporation of the labeled methanol carbon into TCA-cycle derived metabolites. The label can be further enriched by deleting the gene araD that competes with ribulose-5-phosphate.

¹³C carbon derived from labeled methanol provided in the experiment was found to be significantly enriched in the metabolites pyruvate, lactate, succinate, fumarate, malate, glutamate and citrate, but only in the strain expressing both catalytically active MeDH 2315L and the HPS-PHI fusion 2616A together (data not shown). Moreover, this strain grew significantly better than the strain expressing catalytically active MeDH but lacking expression of the HPS-PHI fusion (data not shown), suggesting that the HPS-PHI enzyme is capable of reducing growth inhibitory levels of formaldehyde that cannot be detoxified by other means in this strain background. These results show that co-expression of an active MeDH and the enzymes of the RuMP pathway can effectively assimilate methanol derived carbon and channel it into TCA-cycle derived products.

Example IX Decarboxylation of 2,4-Pentadienoate to Butadiene by a Phenylacrylate Decarboxylase

PadA1 (GI number 1165293) and OhbA1 (GI number 188496963) encoding phenylacrylate decarboxylase from S. cerevisiae were codon optimized by DNA 2.0 and were cloned by DNA 2.0 into the following vectors suitable for expression in E. coli, pD424-NH and pD441-NH respectively (DNA 2.0 Inc.). The genes were tested for decarboxylation of 2,4-pentadienoate and the enzymatic reactions were carried out under the following conditions: 100 mM Tris-HCL pH 7.2; 10 mM KCL; 10 mM NaCL; 5 mM DTT; 20 mM 2,4-Pentadienoate; 1.5 mg/ml lysate of E. coli DH5α cells containing decarboxylase from S. cerevisiae.

The control reactions with lysate in the absence of substrate were conducted in parallel. 100 μL reactions were incubated overnight with shaking (175 rpm) at 25° C. in 1.5 ml gas-tight vials. Headspace GCMS analysis was carried out on a 7890A GC with 5975C inert MSD using a GS-GASPRO column, 30m×0.32 mm (Agilent Technologies). Static headspace sample introduction was performed on a CombiPAL autosampler (CTC Analytics) following 2 min incubation at 45C. The presence of 1,3-butadiene was evaluated and the enzymatic reaction product was identified by direct comparison with a standard of 1,3-butadiene (Sigma). GC/MS analysis showed the production of 1,3-butadiene from the enzymatic samples but not from the lysate alone controls.

While no butadiene formation was detected with the no substrate-control, butadiene was measured when 2,4-PD was added as a substrate (data not shown).

Example X Demonstration of Acetyl-CoA Reductase, 4-hydroxy 2-oxovalerate aldolase, 4-hydroxy 2-oxovalerate Decarboxylase in FIG. 1

Genes expressing acetyl-CoA reductase (bphJ from Burkholderia xenovorans LB400, GI no: 520923), 4-hydroxy 2-oxovalerate aldolase (bphI from Burkholderia xenovorans LB400, GI no: 520924), 4-hydroxy 2-oxovalerate decarboxylase (kdc from Mycobacterium tuberculosis BcG H37Rv, GI no: 614088617), and alcohol dehydrogenase (yjgB from Chronobacter sakazakii, GI no: 387852894) were cloned into a plasmid suitable for expression in E. coli, plasmid pZA23S (kanamycin resistance marker, p15A origin of replication) obtained from R. Lutz (Expressys, Germany) and are based on the pZ Expression System (Lutz, R & Bujard, H. Nucleic Acids Res. 25, 1203-1210 (1997)).

E. coli (MG1655 variants) cells were transformed with the expression plasmid and selected and maintained using antibiotic selection with Kanamycin. Cells were grown in LB media with kanamycin. The formation of a 4-carbon diol from glucose was detected using LCMS while the empty vector control did not make any 4-carbon diol (data not shown).

Example XI Hydrogen Synthesis

Reducing equivalents generated by degradation and metabolism of organic substrates can be harnessed to drive the synthesis of hydrogen (H₂) from protons by a hydrogenase or formate-hydrogen lyase. Reducing equivalents for hydrogen evolution can come in the form of NADH, NADPH, FADH, reduced quinones, reduced ferredoxins, reduced flavodoxins and reduced thioredoxins. The reducing equivalents, particularly quinones and ferredoxins, can directly serve as electron donors for the hydrogen-forming enzymes. For example, electrons from a menaquinol-forming enzyme such as formate dehydrogenase-O can be directly transferred to a menaquinol-utilizing hydrogenase such as hydrogenase-2 of E. coli. Alternately, reducing equivalents can be transferred indirectly via intermediate enzymes that interconvert donor/acceptor pairs to an appropriate reduced cofactor for the hydrogen-forming enzymes. As an example of an indirect electron transfer to hydrogen, electrons from NADH can be transferred to the quinone pool by an NADH dehydrogenase, and the resulting reduced quinones can drive conversion of protons to hydrogen by hydrogenase-2. Enzymes such as NAD(P)H:ferredoxin oxidoreductase are also useful for interconverting redox from NAD(P)H to ferredoxin.

Hydrogenase

Native to E. coli and other enteric bacteria are multiple genes encoding up to four hydrogenases (Sawers, G., Antonie Van Leeuwenhoek 66:57-88 (1994); Sawers et al., J. Bacteriol 164:1324-1331(1985); Sawers and Boxer, Eur. J Biochem. 156:265-275 (1986); Sawers et al., J. Bacteriol 168:398-404 (1986)). Three of the four hydrogenases of E. coli are capable of evolving hydrogen: hydrogenases 2, 3 and 4. The oxygen-sensitive hydrogenase 2 (Hyd-2), encoded by the hybOABCDEFG gene cluster, is membrane-bound and can operate both as an uptake hydrogenase and also in the hydrogen-generating direction (Lukey et al, JBC 285(6):3928-38 (2010)). Hyd-2 transfers electrons to the periplasmic ferredoxin hybA which, in turn, transfers electrons to a quinone via the hybB integral membrane protein. Hydrogenase 3 (hyd-3) is a H2-evolving, energy conserving, membrane-associated hydrogenase responsible for formate-dependent H₂ evolution (Hakobyan et al, Biophys Chem 115:55-61(2005)). Active under anaerobic conditions in the absence of an external electron acceptor, this enzyme is associated with the formate hydrogen lyase complex which converts formate to CO₂ and H₂. The function of hydrogenase 4 (hyf) is unknown but is thought to catalyze a similar reaction to hydrogenase 3 based on sequence similarity and induction under similar conditions. Hydrogenase 3 and 4 are encoded by the hyc and hyf gene clusters, respectively. Hydrogenase activity in E. coli is also dependent upon the expression of the hyp genes whose corresponding proteins are involved in the assembly of the hydrogenase complexes (Jacobi et al., Arch. Microbiol 158:444-451(1992); Rangarajan et al., J. Bacteriol. 190:1447-1458 (2008)). The formate dehydrogenase component of the E. coli formate-hydrogen lyase consists of formate dehydrogenase-H (Maeda et al., Appl Microbiol Biotechnol 77:879-890 (2007)). FHL is activated by the gene product of fhlA (Maeda et al., Appl Microbiol Biotechnol 77:879-890 (2007)). The addition of the trace elements, selenium, nickel and molybdenum, to a fermentation broth has been shown to enhance formate hydrogen lyase activity (Soini et al., Microb. Cell Fact. 7:26 (2008)). These proteins are identified below.

Protein GenBank ID GI Number Organism Hydrogenase-2 HybO AAC76033.1 1789371 Escherichia coli HybA AAC76032.1 1789370 Escherichia coli HybB AAC76031.1 2367183 Escherichia coli HybC AAC76030.1 1789368 Escherichia coli HybD AAC76029.1 1789367 Escherichia coli HybE AAC76028.1 1789366 Escherichia coli HybF AAC76027.1 1789365 Escherichia coli HybG AAC76026.1 1789364 Escherichia coli Hydrogenase-3 HycA NP_417205 16130632 Escherichia coli HycB NP_417204 16130631 Escherichia coli HycC NP_417203 16130630 Escherichia coli HycD NP_417202 16130629 Escherichia coli HycE NP_417201 16130628 Escherichia coli HycF NP_417200 16130627 Escherichia coli HycG NP_417199 16130626 Escherichia coli HycH NP_417198 16130625 Escherichia coli HycI NP_417197 16130624 Escherichia coli Hydrogenase-4 HyfA NP_416976 90111444 Escherichia coli Hyfb NP_416977 16130407 Escherichia coli HyfC NP_416978 90111445 Escherichia coli HyfD NP_416979 16130409 Escherichia coli HyfE NP_416980 16130410 Escherichia coli HyfF NP_416981 16130411 Escherichia coli HyfG NP_416982 16130412 Escherichia coli HyfH NP_416983 16130413 Escherichia coli HyfI NP_416984 16130414 Escherichia coli HyfJ NP_416985 90111446 Escherichia coli HyfR NP_416986 90111447 Escherichia coli Accessory/assembly proteins HypA NP_417206 16130633 Escherichia coli HypB NP_417207 16130634 Escherichia coli HypC NP_417208 16130635 Escherichia coli HypD NP_417209 16130636 Escherichia coli HypE NP_417210 226524740 Escherichia coli HypF NP_417192 16130619 Escherichia coli Formate dehydrogenases and activator fdhF NP_418503 16131905 Escherichia coli fhlA NP_417211 16130638 Escherichia coli fdnG NP_415991.1 16129433 Escherichia coli fdnH NP_415992.1 16129434 Escherichia coli fdnI NP_415993.1 16129435 Escherichia coli fdoG NP_418330.1 16131734 Escherichia coli fdoH NP_418329.1 16131733 Escherichia coli fdoI NP_418328.1 16131732 Escherichia coli Formate-Hydrogen Lyase

A formate hydrogen lyase enzyme also exists in the hyperthermophilic archaeon, Thermococcus litoralis (Takacs et al., BMC. Microbiol 8:88 (2008)). Additional formate hydrogen lyase systems have been found in Salmonella typhimurium, Klebsiella pneumoniae, Rhodospirillum rubrum, Methanobacterium formicicum (Vardar-Schara et al., 1:107-125 (2008)). These proteins are identified below.

Protein GenBank ID GI Number Organism mhyC ABW05543 157954626 Thermococcus litoralis mhyD ABW05544 157954627 Thermococcus litoralis mhyE ABW05545 157954628 Thermococcus litoralis myhF ABW05546 157954629 Thermococcus litoralis myhG ABW05547 157954630 Thermococcus litoralis myhH ABW05548 157954631 Thermococcus litoralis fdhA AAB94932 2746736 Thermococcus litoralis fdhB AAB94931 157954625 Thermococcus litoralis

Alternately, an NADH-dependent hydrogenase can be utilized. Bidirectional NADH-dependent hydrogenases have been characterized in cyanobacteria such as Synechocystis sp. PCC 6803 and proteobacteria such as Cupriavidus necator (Schmitz et al, Biochem Biophys Acta 1554:66-74 (2002)). The C. necator (R. eutropha H16) hydrogenase is O₂-tolerant, cytoplasmic and directly transfers electrons from NADH to hydrogen (Schneider and Schlegel, Biochim. Biophys. Acta 452, 66-80 (1976); Burgdorf, J. Bact. 187(9) 3122-3132(2005)). Soluble hydrogenase enzymes are additionally present in several other organisms including Geobacter sulfurreducens (Coppi, Microbiology 151, 1239-1254 (2005)), Synechocystis str. PCC 6803 (Genner, J. Biol. Chem., 284(52), 36462-36472 (2009)), and Thiocapsa roseopersicina (Rakhely, Appl. Environ. Microbiol. 70(2) 722-728 (2004)). The Synechocystis enzyme is capable of generating NADPH from hydrogen. Overexpression of both the Hox operon from Synechocystis str. PCC 6803 and the accessory genes encoded by the Hyp operon from Nostoc sp. PCC 7120 led to increased hydrogenase activity compared to expression of the Hox genes alone (Germer, J. Biol. Chem. 284(52), 36462-36472 (2009)).

Protein GenBank ID GI Number Organism HoxF NP_942727.1 38637753 Ralstonia eutropha H16 HoxU NP_942728.1 38637754 Ralstonia eutropha H16 HoxY NP_942729.1 38637755 Ralstonia eutropha H16 HoxH NP_942730.1 38637756 Ralstonia eutropha H16 HoxW NP_942731.1 38637757 Ralstonia eutropha H16 HoxI NP_942732.1 38637758 Ralstonia eutropha H16 HoxE NP_953767.1 39997816 Geobacter sulfurreducens HoxF NP_953766.1 39997815 Geobacter sulfurreducens HoxU NP_953765.1 39997814 Geobacter sulfurreducens HoxY NP_953764.1 39997813 Geobacter sulfurreducens HoxH NP_953763.1 39997812 Geobacter sulfurreducens GSU2717 NP_953762.1 39997811 Geobacter sulfurreducens HoxE NP_441418.1 16330690 Synechocystis str. PCC 6803 HoxF NP_441417.1 16330689 Synechocystis str. PCC 6803 Unknown function NP_441416.1 16330688 Synechocystis str. PCC 6803 HoxU NP_441415.1 16330687 Synechocystis str. PCC 6803 HoxY NP_441414.1 16330686 Synechocystis str. PCC 6803 Unknown function NP_441413.1 16330685 Synechocystis str. PCC 6803 Unknown function NP_441412.1 16330684 Synechocystis str. PCC 6803 HoxH NP_441411.1 16330683 Synechocystis str. PCC 6803 HypF NP_484737.1 17228189 Nostoc sp. PCC 7120 HypC NP_484738.1 17228190 Nostoc sp. PCC 7120 HypD NP_484739.1 17228191 Nostoc sp. PCC 7120 Unknown function NP_484740.1 17228192 Nostoc sp. PCC 7120 HypE NP_484741.1 17228193 Nostoc sp. PCC 7120 HypA NP_484742.1 17228194 Nostoc sp. PCC 7120 HypB NP_484743.1 17228195 Nostoc sp. PCC 7120 Hox1E AAP50519.1 37787351 Thiocapsa roseopersicina Hox1F AAP50520.1 37787352 Thiocapsa roseopersicina Hox1U AAP50521.1 37787353 Thiocapsa roseopersicina Hox1Y AAP50522.1 37787354 Thiocapsa roseopersicina Hox1H AAP50523.1 37787355 Thiocapsa roseopersicina

Genes encoding hydrogenase enzymes from C. ljungdahli are shown below.

Protein GenBank ID GI Number Organism CLJU c20290 ADK15091.1 300435324 Clostridium ljungdahli CLJU c07030 ADK13773.1 300434006 Clostridium ljungdahli CLJU c07040 ADK13774.1 300434007 Clostridium ljungdahli CLJU_c07050 ADK13775.1 300434008 Clostridium ljungdahli CLJU_c07060 ADK13776.1 300434009 Clostridium ljungdahli CLJU c07070 ADK13777.1 300434010 Clostridium ljungdahli CLJU c07080 ADK13778.1 300434011 Clostridium ljungdahli CLJU_c14730 ADK14541.1 300434774 Clostridium ljungdahli CLJU_c14720 ADK14540.1 300434773 Clostridium ljungdahli CLJU c14710 ADK14539.1 300434772 Clostridium ljungdahli CLJU c14700 ADK14538.1 300434771 Clostridium ljungdahli CLJU_c28670 ADK15915.1 300436148 Clostridium ljungdahli CLJU_c28660 ADK15914.1 300436147 Clostridium ljungdahli CLJU_c28650 ADK15913.1 300436146 Clostridium ljungdahli CLJU_c28640 ADK15912.1 300436145 Clostridium ljungdahli

The M. thermoacetica hydrogenases are suitable for a host that lacks sufficient endogenous hydrogenase activity. M. thermoacetica can grow with CO₂ as the exclusive carbon source indicating that reducing equivalents are extracted from H2 to enable acetyl-CoA synthesis via the Wood-Ljungdahl pathway (Drake, H. L., J. Bacteriol. 150:702-709 (1982); Drake and Daniel, Res. Microbiol. 155:869-883 (2004); Kellum and Drake, J. Bacteriol. 160:466-469 (1984)) (see FIG. 68). M. thermoacetica has homologs to several hyp, hyc, and hyf genes from E. coli. The protein sequences encoded for by these genes are identified by the following GenBank accession numbers.

Protein GenBank ID GI Number Organism Moth_2175 YP_431007 83590998 Moorella thermoacetica Moth 2176 YP_431008 83590999 Moorella thermoacetica Moth 2177 YP_431009 83591000 Moorella thermoacetica Moth 2178 YP_431010 83591001 Moorella thermoacetica Moth_2179 YP_431011 83591002 Moorella thermoacetica Moth_2180 YP_431012 83591003 Moorella thermoacetica Moth 2181 YP_431013 83591004 Moorella thermoacetica Moth 2182 YP_431014 83591005 Moorella thermoacetica Moth_2183 YP_431015 83591006 Moorella thermoacetica Moth_2184 YP_431016 83591007 Moorella thermoacetica Moth_2185 YP_431017 83591008 Moorella thermoacetica Moth 2186 YP_431018 83591009 Moorella thermoacetica Moth 2187 YP_431019 83591010 Moorella thermoacetica Moth_2188 YP_431020 83591011 Moorella thermoacetica Moth_2189 YP_431021 83591012 Moorella thermoacetica Moth 2190 YP_431022 83591013 Moorella thermoacetica Moth 2191 YP_431023 83591014 Moorella thermoacetica Moth 2192 YP_431024 83591015 Moorella thermoacetica Moth_0439 YP_429313 83589304 Moorella thermoacetica Moth_0440 YP_429314 83589305 Moorella thermoacetica Moth 0441 YP_429315 83589306 Moorella thermoacetica Moth 0442 YP_429316 83589307 Moorella thermoacetica Moth 0809 YP_429670 83589661 Moorella thermoacetica Moth_0810 YP_429671 83589662 Moorella thermoacetica Moth_0811 YP_429672 83589663 Moorella thermoacetica Moth 0812 YP_429673 83589664 Moorella thermoacetica Moth 0814 YP_429674 83589665 Moorella thermoacetica Moth_0815 YP_429675 83589666 Moorella thermoacetica Moth_0816 YP_429676 83589667 Moorella thermoacetica Moth_1193 YP_430050 83590041 Moorella thermoacetica Moth 1194 YP_430051 83590042 Moorella thermoacetica Moth 1195 YP_430052 83590043 Moorella thermoacetica Moth_1196 YP_430053 83590044 Moorella thermoacetica Moth_1717 YP_430562 83590553 Moorella thermoacetica Moth 1718 YP_430563 83590554 Moorella thermoacetica Moth 1719 YP_430564 83590555 Moorella thermoacetica Moth 1883 YP_430726 83590717 Moorella thermoacetica Moth_1884 YP_430727 83590718 Moorella thermoacetica Moth_1885 YP_430728 83590719 Moorella thermoacetica Moth 1886 YP_430729 83590720 Moorella thermoacetica Moth 1887 YP_430730 83590721 Moorella thermoacetica Moth_1888 YP_430731 83590722 Moorella thermoacetica Moth_1452 YP_430305 83590296 Moorella thermoacetica Moth_1453 YP_430306 83590297 Moorella thermoacetica Moth_1454 YP_430307 83590298 Moorella thermoacetica

Genes encoding hydrogenase enzymes from C. ljungdahli are shown below.

Protein GenBank ID GI Number Organism CLJU c20290 ADK15091.1 300435324 Clostridium ljungdahli CLJU c07030 ADK13773.1 300434006 Clostridium ljungdahli CLJU_c07040 ADK13774.1 300434007 Clostridium ljungdahli CLJU_c07050 ADK13775.1 300434008 Clostridium ljungdahli CLJU_c07060 ADK13776.1 300434009 Clostridium ljungdahli CLJU c07070 ADK13777.1 300434010 Clostridium ljungdahli CLJU c07080 ADK13778.1 300434011 Clostridium ljungdahli CLJU_c14730 ADK14541.1 300434774 Clostridium ljungdahli CLJU_c14720 ADK14540.1 300434773 Clostridium ljungdahli CLJU c14710 ADK14539.1 300434772 Clostridium ljungdahli CLJU c14700 ADK14538.1 300434771 Clostridium ljungdahli CLJU c28670 ADK15915.1 300436148 Clostridium ljungdahli CLJU_c28660 ADK15914.1 300436147 Clostridium ljungdahli CLJU_c28650 ADK15913.1 300436146 Clostridium ljungdahli CLJU_c28640 ADK15912.1 300436145 Clostridium ljungdahli Ferredoxin:NADP+ Oxidoreductase

For enzymes that use reducing equivalents in the form of NADH or NADPH, these reduced Gathers can be generated by transferring electrons from reduced ferredoxin. Two enzymes catalyze the reversible transfer of electrons from reduced ferredoxins to NAD(P)⁺, ferredoxin:NAD⁺ oxidoreductase (EC 1.18.1.3) and ferredoxin:NADP⁺ oxidoreductase (FNR, EC 1.18.1.2). Ferredoxin:NADP⁺ oxidoreductase (FNR, EC 1.18.1.2) has a noncovalently bound FAD cofactor that facilitates the reversible transfer of electrons from NADPH to low-potential acceptors such as ferredoxins or flavodoxins (Blaschkowski et al, Eur. J. Biochem. 123:563-569 (1982); Fujii et al., 1977). The Helicobacter pylori FNR, encoded by HP1164 (fqrB), is coupled to the activity of pyruvate:ferredoxin oxidoreductase (PFOR) resulting in the pyruvate-dependent production of NADPH (St Maurice et al., J. Bacteriol. 189:4764-4773 (2007)). An analogous enzyme is found in Campylobacter jejuni (St Maurice et al., J. Bacteriol. 189:4764-4773 (2007)). A ferredoxin:NADP⁺ oxidoreductase enzyme is encoded in the E. coli genome by fpr (Bianchi et al. J Bacteriol. 1993 March; 175(6):1590-5). Ferredoxin:NAD⁺ oxidoreductase utilizes reduced ferredoxin to generate NADH from NAD⁺. In several organisms, including E. coli, this enzyme is a component of multifunctional dioxygenase enzyme complexes. The ferredoxin:NAD⁺ oxidoreductase of E. coli, encoded by hcaD, is a component of the 3-phenylproppionate dioxygenase system involved in involved in aromatic acid utilization (Diaz et al. J. Bacteriol. 1998 June; 180(11):2915-23). NADH:ferredoxin reductase activity was detected in cell extracts of Hydrogenobacter thermophilus strain TK-6, although a gene with this activity has not yet been indicated (Yoon et al. Arch Microbiol. 1997 May; 167(5):275-9). NADP oxidoreductase of C. kluyveri, encoded by nfnAB, catalyzes the concomitant reduction of ferredoxin and NAD+ with two equivalents of NADPH (Wang et al, J Bacteriol 192: 5115-5123 (2010)). Finally, the energy-conserving membrane-associated Rnf-type proteins (Seedorf et al., Proc. Natl. Acad. Sci. U.S.A. 105:2128-2133 (2008); Herrmann et al., J. Bacteriol. 190:784-791 (2008)) provide a means to generate NADH or NADPH from reduced ferredoxin. Additional ferredoxin:NAD(P)+ oxidoreductases have been annotated in Clostridium carboxydivorans P7 and Clostridium ljungdahli.

Protein GenBank ID GI Number Organism HP1164 NP_207955.1 15645778 Helicobacter pylori RPA3954 CAE29395.1 39650872 Rhodopseudomonas palustris fpr BAH29712.1 225320633 Hydrogenobacter thermophilus yumC NP_391091.2 255767736 Bacillus subtilis CJE0663 AAW35824.1 57167045 Campylobacter jejuni fpr P28861.4 399486 Escherichia coli hcaD AAC75595.1 1788892 Escherichia coli LOC100282643 NP_001149023.1 226497434 Zea mays NfnA YP_001393861.1 153953096 Clostridium kluyveri NfnB YP_001393862.1 153953097 Clostridium kluyveri RnfC EDK33306.1 146346770 Clostridium kluyveri RnfD EDK33307.1 146346771 Clostridium kluyveri RnfG EDK33308.1 146346772 Clostridium kluyveri RnfE EDK33309.1 146346773 Clostridium kluyveri RnfA EDK33310.1 146346774 Clostridium kluyveri RnfB EDK33311.1 146346775 Clostridium kluyveri CcarbDRAFT_2639 ZP_05392639.1 255525707 Clostridium carboxidivorans P7 CcarbDRAFT 2638 ZP_05392638.1 255525706 Clostridium carboxidivorans P7 CcarbDRAFT 2636 ZP_05392636.1 255525704 Clostridium carboxidivorans P7 CcarbDRAFT_5060 ZP_05395060.1 255528241 Clostridium carboxidivorans P7 CcarbDRAFT_2450 ZP_05392450.1 255525514 Clostridium carboxidivorans P7 CcarbDRAFT 1084 ZP_05391084.1 255524124 Clostridium carboxidivorans P7 CLJU c11410 (RnfB) ADK14209.1 300434442 Clostridium ljungdahli CLJU c11400 (RnfA) ADK14208.1 300434441 Clostridium ljungdahli CLJU_c11390 (RnfE) ADK14207.1 300434440 Clostridium ljungdahli CLJU_c11380 (RnfG) ADK14206.1 300434439 Clostridium ljungdahli CLJU c11370 (RnfD) ADK14205.1 300434438 Clostridium ljungdahli CLJU c11360 (RnfC) ADK14204.1 300434437 Clostridium ljungdahli

Ferredoxins are small acidic proteins containing one or more iron-sulfur clusters that function as intracellular electron Gathers with a low reduction potential. Reduced ferredoxins donate electrons to Fe-dependent enzymes such as ferredoxin-NADP⁺ oxidoreductase, pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OFOR). The H. thermophilus gene fdx1 encodes a [4Fe-4S]-type ferredoxin that is required for the reversible carboxylation of 2-oxoglutarate and pyruvate by OFOR and PFOR, respectively (Yamamoto et al., Extremophiles 14:79-85 (2010)). The ferredoxin associated with the Sulfolobus solfataricus 2-oxoacid:ferredoxin reductase is a monomeric dicluster [3Fe-4S][4Fe-4S]-type ferredoxin (Park et al. J Biochem Mol Biol. 2006 Jan. 31; 39(1):46-54). While the N-terminal domain of the protein shares 93% homology with the zfx ferredoxin from S. acidocaldarius. The E. coli genome encodes a soluble ferredoxin of unknown physiological function, fdx. Some evidence indicates that this protein can function in iron-sulfur cluster assembly (Takahashi and Nakamura, J Biochem. 1999 November; 126(5):917-26). Additional ferredoxin proteins have been characterized in Helicobacter pylori (Mukhopadhyay et al. J. Bacteriol. 2003 May; 185(9):2927-35) and Campylobacter jejuni (van Vliet et al. FEMS Microbiol Lett. 2001 Mar. 15; 196(2):189-93). A 2Fe-2S ferredoxin from Clostridium pasteurianum has been cloned and expressed in E. coli (Fujinaga and Meyer, Biochemical and Biophysical Research Communications, 192(3): (1993)). Acetogenic bacteria such as Moorella thermoacetica, Clostridium carboxidivorans P7, Clostridium ljungdahli and Rhodospirillum rubrum are predicted to encode several ferredoxins, listed in the table below.

Protein GenBank ID GI Number Organism fdx1 BAE02673.1 68163284 Hydrogenobacter thermophilus M11214.1 AAA83524.1 144806 Clostridium pasteurianum Zfx AAY79867.1 68566938 Sulfolobus acidocalarius Fdx AAC75578.1 1788874 Escherichia coli hp 0277 AAD07340.1 2313367 Helicobacter pylori fdxA CAL34484.1 112359698 Campylobacter jejuni Moth 0061 ABC18400.1 83571848 Moorella thermoacetica Moth_1200 ABC19514.1 83572962 Moorella thermoacetica Moth_1888 ABC20188.1 83573636 Moorella thermoacetica Moth 2112 ABC20404.1 83573852 Moorella thermoacetica Moth_1037 ABC19351.1 83572799 Moorella thermoacetica CcarbDRAFT_4383 ZP_05394383.1 255527515 Clostridium carboxidivorans P7 CcarbDRAFT_2958 ZP_05392958.1 255526034 Clostridium carboxidivorans P7 CcarbDRAFT_2281 ZP_05392281.1 255525342 Clostridium carboxidivorans P7 CcarbDRAFT_5296 ZP_05395295.1 255528511 Clostridium carboxidivorans P7 CcarbDRAFT_1615 ZP_05391615.1 255524662 Clostridium carboxidivorans P7 CcarbDRAFT_1304 ZP_05391304.1 255524347 Clostridium carboxidivorans P7 cooF AAG29808.1 11095245 Carboxydothermus hydrogenoformans fdxN CAA35699.1 46143 Rhodobacter capsulatus Rru_A2264 ABC23064.1 83576513 Rhodospirillum rubrum Rru_A1916 ABC22716.1 83576165 Rhodospirillum rubrum Rru_A2026 ABC22826.1 83576275 Rhodospirillum rubrum cooF AAC45122.1 1498747 Rhodospirillum rubrum fdxN AAA26460.1 152605 Rhodospirillum rubrum Alvin_2884 ADC63789.1 288897953 Allochromatium vinosum DSM 180 fdx YP_002801146.1 226946073 Azotobacter vinelandii DJ CKL_3790 YP_001397146.1 153956381 Clostridium kluyveri DSM 555 fer1 NP_949965.1 39937689 Rhodopseudomonas palustris CGA009 fdx CAA12251.1 3724172 Thauera aromatica CHY_2405 YP_361202.1 78044690 Carboxydothermus hydrogenoformans fer YP_359966.1 78045103 Carboxydothermus hydrogenoformans fer AAC83945.1 1146198 Bacillus subtilis fdx1 NP_249053.1 15595559 Pseudomonas aeruginosa PA01 yfhL AP_003148.1 89109368 Escherichia coli K-12 CLJU c00930 ADK13195.1 300433428 Clostridium ljungdahli CLJU_c00010 ADK13115.1 300433348 Clostridium ljungdahli CLJU_c01820 ADK13272.1 300433505 Clostridium ljungdahli CLJU c17980 ADK14861.1 300435094 Clostridium ljungdahli CLJU c17970 ADK14860.1 300435093 Clostridium ljungdahli CLJU c22510 ADK15311.1 300435544 Clostridium ljungdahli CLJU_c26680 ADK15726.1 300435959 Clostridium ljungdahli CLJU_c29400 ADK15988.1 300436221 Clostridium ljungdahli

Throughout this application various publications have been referenced. The disclosures of these publications in their entireties, including GenBank and GI number publications, are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this invention pertains. Although the invention has been described with reference to the examples provided above, it should be understood that various modifications can be made without departing from the spirit of the invention. 

What is claimed is:
 1. A non-naturally occurring microbial organism, said microbial organism having a butadiene pathway and comprising at least four exogenous nucleic acids encoding butadiene pathway enzyme expressed in a sufficient amount to produce butadiene, wherein said butadiene pathway comprises a pathway selected from: (9) 1B, 1C, 1G, 1I, 1L, 1M, and 1F; (10) 1B, 1C, 1G, 1I, 1L, 1N, and 1F; (11) 1B, 1C, 1H, 1I, 1L, 1M, and 1F; (12) 1B, 1C, 1H, 1I, 1L, 1N, and 1F; (13) 1B, 1C, 1D, 1J, 1L, 1M, and 1F; (14) 1B, 1C, 1D, 1J, 1L, 1N, and 1F; (15) 1B, 1C, 1D, 1K, 1L, 1M, and 1F; and (16) 1B, 1C, 1D, 1K, 1L, 1N, and 1F, wherein 1B is a 4-hydroxy 2-oxovalerate aldolase, wherein 1C is a 4-hydroxy 2-oxovalerate dehydratase, wherein 1D is a 2-oxopentenoate reductase, wherein 1F is a 2,4-pentadienoate decarboxylase, wherein 1G is a 2-oxopentenoate ligase, wherein 1H is a 2-oxopentenoate:acetyl CoA CoA transferase, wherein 1I is a 2-oxopentenoyl-CoA reductase, wherein 1J is a 2-hydroxypentenoate ligase, wherein 1K is a 2-hydroxypentenoate:acetyl-CoA CoA transferase, wherein 1L is a 2-hydroxypentenoyl-CoA dehydratase, wherein 1M is a 2,4-Pentadienoyl-CoA hydrolase, and wherein 1N is a 2,4-Pentadienoyl-CoA:acetyl CoA CoA transferase.
 2. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism comprises one, two, three, four, five, six, seven, eight, nine, ten, or eleven exogenous nucleic acids each encoding a butadiene pathway enzyme, or wherein said microbial organism comprises exogenous nucleic acids encoding each of the enzymes of at least one of the pathways selected from (9)-(16).
 3. The non-naturally occurring microbial organism of claim 1 further comprising an acetyl-CoA pathway, wherein said acetyl-CoA pathway comprises a pathway selected from: (1) 3T and 3V; (2) 3T, 3W, and 3X; (3) 3U and 3V; (4) 3U, 3W, and 3X wherein 3T is a fructose-6-phosphate phosphoketolase, wherein 3U is a xylulose-5-phosphate phosphoketolase, wherein 3V is a phosphotransacetylase, wherein 3W is an acetate kinase, wherein 3X is an acetyl-CoA transferase, an acetyl-CoA synthetase, or an acetyl-CoA ligase.
 4. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism further comprises a formaldehyde fixation pathway, wherein said formaldehyde fixation pathway comprises: (1) 3D and 3Z; (2) 3D; or (3) 3B and 3C, wherein 3B is a 3-hexulose-6-phosphate synthase, wherein 3C is a 6-phospho-3-hexuloisomerase, wherein 3D is a dihydroxyacetone synthase, wherein 3Z is a fructose-6-phosphate aldolase.
 5. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism further comprises a methanol metabolic pathway, wherein said methanol metabolic pathway comprises a pathway selected from: (1) 4A and 4B; (2) 4A, 4B and 4C; (3) 4J; (4) 4J, 4K and 4C; (5) 4J, 4M, and 4N; (6) 4J and 4L; (7) 4J, 4L, and 4G; (8) 4J, 4L, and 4I; (9) 4A, 4B, 4C, 4D, and 4E; (10) 4A, 4B, 4C, 4D, and 4F; (11) 4J, 4K, 4C, 4D, and 4E; (12) 4J, 4K, 4C, 4D, and 4F; (13) 4J, 4M, 4N, and 4O; (14) 4A, 4B, 4C, 4D, 4E, and 4G; (15) 4A, 4B, 4C, 4D, 4F, and 4G; (16) 4J, 4K, 4C, 4D, 4E, and 4G; (17) 4J, 4K, 4C, 4D, 4F, and 4G; (18) 4J, 4M, 4N, 4O, and 4G; (19) 4A, 4B, 4C, 4D, 4E, and 4I; (20) 4A, 4B, 4C, 4D, 4F, and 4I; (21) 4J, 4K, 4C, 4D, 4E, and 4I; (22) 4J, 4K, 4C, 4D, 4F, and 4I; and (23) 4J, 4M, 4N, 4O, and 4I, wherein 4A is a methanol methyltransferase, wherein 4B is a methylenetetrahydrofolate reductase, wherein 4C is a methylenetetrahydrofolate dehydrogenase, wherein 4D is a methenyltetrahydrofolate cyclohydrolase, wherein 4E is a formyltetrahydrofolate deformylase, wherein 4F is a formyltetrahydrofolate synthetase, wherein 4G is a formate hydrogen lyase, wherein 4I is a formate dehydrogenase, wherein 4J is a methanol dehydrogenase, wherein 4K is a formaldehyde activating enzyme or spontaneous, wherein 4L is a formaldehyde dehydrogenase, wherein 4M is a S-(hydroxymethyl)glutathione synthase or spontaneous, wherein 4N is a glutathione-dependent formaldehyde dehydrogenase, wherein 4O is a S-formylglutathione hydrolase.
 6. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism further comprises a formate assimilation pathway, wherein said formate assimilation pathway comprises a pathway selected from: (1) 3E; (2) 3F, and 3G; (3) 3H, 3I, 3J, and 3K; (4) 3H, 3I, 3J, 3L, 3M, and 3N; (5) 3E, 3H, 3I, 3J, 3L, 3M, and 3N; (6) 3F, 3G, 3H, 3I, 3J, 3L, 3M, and 3N; (7) 3K, 3H, 3I, 3J, 3L, 3M, and 3N; and (8) 3H, 3I, 3J, 3O, and 3P, wherein 3E is a formate reductase, 3F is a formate ligase, a formate transferase, or a formate synthetase, wherein 3G is a formyl-CoA reductase, wherein 3H is a formyltetrahydrofolate synthetase, wherein 3I is a methenyltetrahydrofolate cyclohydrolase, wherein 3J is a methylenetetrahydrofolate dehydrogenase, wherein 3K is a formaldehyde-forming enzyme or spontaneous, wherein 3L is a glycine cleavage system, wherein 3M is a serine hydroxymethyltransferase, wherein 3N is a serine deaminase, wherein 3O is a methylenetetrahydrofolate reductase, wherein 3P is an acetyl-CoA synthase.
 7. The non-naturally occurring microbial organism of claim 6, wherein said formate assimilation pathway further comprises: (1) 3Q; (2) 3R and 3S; (3) 3Y and 3Q; or (4) 3Y, 3R, and 3S, wherein 3Q is a pyruvate formate lyase, wherein 3R is a pyruvate dehydrogenase, a pyruvate ferredoxin oxidoreductase, or a pyruvate:NADP+oxidoreductase, wherein 3S is a formate dehydrogenase, wherein 3Y is a glyceraldehyde-3-phosphate dehydrogenase or an enzyme of lower glycolysis.
 8. The non-naturally occurring microbial organism of claim 1, wherein said organism further comprises: (a) a methanol oxidation pathway, wherein said methanol oxidation pathway comprises 3A, wherein 3A a methanol dehydrogenase; (b) a carbon monoxide dehydrogenase; (c) a hydrogenase; (d) attenuation of one or more endogenous enzymes selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof; (e) attenuation of one or more endogenous enzymes of a competing formaldehyde assimilation or dissimilation pathway; (f) a gene disruption of one or more endogenous nucleic acids encoding enzymes selected from DHA kinase, methanol oxidase, PQQ-dependent methanol dehydrogenase, DHA synthase or any combination thereof, (g) a gene disruption of one or more endogenous nucleic acids encoding enzymes of a competing formaldehyde assimilation or dissimilation pathway; or (h) a hydrogen synthesis pathway catalyzing the synthesis of hydrogen from a reducing equivalent, said hydrogen synthesis pathway comprising an enzyme selected from the group consisting of a hydrogenase, a formate-hydrogene lyase and ferredoxin: NADP+ oxidoreductase.
 9. The non-naturally occurring microbial organism of claim 1, wherein said at least one exogenous nucleic acid is a heterologous nucleic acid.
 10. The non-naturally occurring microbial organism of claim 1, wherein said non-naturally occurring microbial organism is in a substantially anaerobic culture medium.
 11. The non-naturally occurring microbial organism of claim 1, wherein said microbial organism is a species of bacteria, yeast, or fungus.
 12. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1G, 1I, 1L, 1M, and 1F.
 13. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1G, 1I, 1L, 1N, and 1F.
 14. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1H, 1I, 1L, 1M, and 1F.
 15. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1H, 1I, 1L, 1N, and 1F.
 16. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1D, 1J, 1L, 1M, and 1F.
 17. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1D, 1J, 1L, 1N, and 1F.
 18. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1D, 1K, 1L, 1M, and 1F.
 19. The non-naturally occurring microbial organism of claim 1, wherein said butadiene pathway comprises 1B, 1C, 1D, 1K, 1L, 1N, and 1F.
 20. A method for producing (a) butadiene or (b) butadiene and hydrogen, comprising culturing the non-naturally occurring microbial organism of claim 1 under conditions and for a sufficient period of time to produce butadiene.
 21. The method of claim 20, wherein said method further comprises separating the butadiene or the butadiene and hydrogen from other components in the culture.
 22. The method of claim 21, wherein the separating comprises extraction, continuous liquid-liquid extraction, pervaporation, membrane filtration, membrane separation, reverse osmosis, electrodialysis, distillation, crystallization, centrifugation, extractive filtration, ion exchange chromatography, absorption chromatography, or ultrafiltration.
 23. A culture medium comprising bioderived butadiene, wherein said culture medium is separated from a non-naturally occurring microbial organism having the butadiene pathway in claim
 1. 